diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index 9225233437..97785d1b18 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -52,6 +52,7 @@ @prefix bioschemas: . @prefix dcat: . @prefix dcid: . +@prefix dcmitype: . @prefix dct: . @prefix fabio: . @prefix foaf: . @@ -66,9 +67,9 @@ @prefix qud: . @prefix rdf: . @prefix rdfs: . -@prefix schema: . +@prefix schema1: . @prefix skos: . -@prefix wgs: . +@prefix wgs1: . @prefix xsd: . a owl:Ontology ; @@ -136,16 +137,16 @@ biolink:AccessibleDnaRegion a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; @@ -158,14 +159,14 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; linkml:attributes "{}" ; @@ -183,21 +184,13 @@ biolink:Bacterium a owl:Class ; biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:Behavior ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; @@ -206,6 +199,14 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:onClass biolink:BehavioralFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; @@ -214,14 +215,14 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:Behavior ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; @@ -267,12 +268,12 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ], + [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; linkml:attributes "{}" ; @@ -282,36 +283,36 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], biolink:Association, biolink:CaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -324,13 +325,13 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:label "causal gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Disease ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Disease ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:EntityToDiseaseAssociationMixin, biolink:GeneToDiseaseAssociation, biolink:GeneToEntityAssociationMixin ; @@ -357,6 +358,10 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onClass biolink:CellLine ; owl:onProperty rdf:subject ; @@ -365,10 +370,6 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin ; @@ -381,28 +382,24 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onClass biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:qualified_predicate ], + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; @@ -413,44 +410,48 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onClass biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:onClass biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onClass linkml:String ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" ; linkml:attributes "{}" ; @@ -480,6 +481,10 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; @@ -488,10 +493,6 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "A regulatory relationship between two genes" ; linkml:attributes "{}" ; @@ -502,19 +503,15 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; @@ -522,27 +519,31 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], biolink:Association, biolink:ChemicalToEntityAssociationMixin ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; @@ -570,18 +571,18 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:ChemicalToChemicalAssociation ; skos:definition """A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: @@ -710,19 +711,19 @@ biolink:ConceptCountAnalysisResult a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:onClass biolink:InformationContentEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Agent ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:InformationContentEntity ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; @@ -813,13 +814,21 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; @@ -827,15 +836,15 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:onClass biolink:Disease ; owl:onProperty rdf:subject ; @@ -844,14 +853,6 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:PhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], biolink:Association, biolink:DiseaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -899,15 +900,15 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:EntityToDiseaseAssociationMixin, biolink:GeneToDiseaseAssociation, @@ -980,13 +981,13 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Exon ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Transcript ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Exon ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" ; linkml:attributes "{}" ; @@ -995,13 +996,13 @@ biolink:ExonToTranscriptRelationship a owl:Class ; biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:temporal_context_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:population_context_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:temporal_context_qualifier ], biolink:Association, biolink:EntityToOutcomeAssociationMixin ; skos:definition "An association between an exposure event and an outcome." ; @@ -1012,29 +1013,21 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:ExposureEvent ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:onClass biolink:ExposureEvent ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; @@ -1042,11 +1035,19 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; @@ -1102,17 +1103,17 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:Disease ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onClass biolink:Disease ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:GeneToDiseaseAssociation ; linkml:attributes "{}" ; linkml:is_a "gene to disease association" . @@ -1120,13 +1121,9 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LifeStage ; @@ -1136,9 +1133,13 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; linkml:attributes "{}" ; @@ -1147,25 +1148,25 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], biolink:GeneExpressionMixin, biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; @@ -1176,6 +1177,10 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1183,10 +1188,6 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; owl:onClass biolink:GeneFamily ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; linkml:attributes "{}" ; @@ -1195,6 +1196,10 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1202,10 +1207,6 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:GeneToGeneAssociation ; skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; linkml:attributes "{}" ; @@ -1214,6 +1215,10 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:GeneProductMixin ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -1221,10 +1226,6 @@ biolink:GeneToGeneProductRelationship a owl:Class ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; linkml:attributes "{}" ; @@ -1249,13 +1250,13 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Pathway ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Pathway ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:GeneToEntityAssociationMixin ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; @@ -1266,13 +1267,13 @@ biolink:GeneToPathwayAssociation a owl:Class ; biolink:GeneToPhenotypeAssociation a owl:Class ; rdfs:label "gene to phenotype association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GeneToDiseaseOrPhenotypicFeatureAssociation, biolink:GeneToEntityAssociationMixin ; @@ -1307,18 +1308,18 @@ biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene_or_gene_product ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], biolink:Attribute, biolink:ExposureEvent, biolink:GeneGroupingMixin, @@ -1372,10 +1373,6 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -1383,6 +1380,10 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; owl:onClass biolink:Genotype ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ; linkml:attributes "{}" ; @@ -1391,6 +1392,10 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], @@ -1398,38 +1403,34 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; @@ -1442,13 +1443,13 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -1570,11 +1571,11 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; @@ -1662,10 +1663,6 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:MaterialSample ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], @@ -1673,6 +1670,10 @@ biolink:MaterialSampleDerivationAssociation a owl:Class ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." ; linkml:attributes "{}" ; @@ -1734,14 +1735,14 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; owl:onClass biolink:Pathway ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:MolecularActivity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; linkml:attributes "{}" ; @@ -1757,21 +1758,21 @@ biolink:MortalityOutcome a owl:Class ; biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -1792,12 +1793,12 @@ biolink:NucleicAcidSequenceMotif a owl:Class ; biolink:NucleosomeModification a owl:Class ; rdfs:label "nucleosome modification" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:LabelType ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LabelType ; + owl:onProperty biolink:synonym ], biolink:BiologicalEntity, biolink:EpigenomicEntity, biolink:GeneProductIsoformMixin, @@ -1822,14 +1823,14 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:OrganismTaxonToEntityAssociation ; linkml:attributes "{}" ; @@ -1839,10 +1840,6 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:associated_environmental_context ], @@ -1854,6 +1851,10 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; linkml:attributes "{}" ; @@ -1862,13 +1863,13 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; owl:onProperty rdf:subject ; @@ -1895,10 +1896,6 @@ biolink:OrganismToOrganismAssociation a owl:Class ; biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], @@ -1910,6 +1907,10 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; owl:onClass biolink:OrganismalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin ; @@ -1921,9 +1922,17 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:object ; @@ -1932,14 +1941,6 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:interacting_molecules_category ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; linkml:attributes "{}" ; @@ -2098,14 +2099,14 @@ biolink:PopulationToPopulationAssociation a owl:Class ; owl:onClass biolink:PopulationOfIndividualOrganisms ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PopulationOfIndividualOrganisms ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a two populations" ; linkml:attributes "{}" ; @@ -2275,9 +2276,9 @@ biolink:Serial a owl:Class ; owl:allValuesFrom linkml:String ; owl:onProperty rdf:type ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -2285,11 +2286,11 @@ biolink:Serial a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], biolink:Publication ; skos:altLabel "journal" ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; @@ -2347,16 +2348,16 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; - rdfs:subClassOf [ a owl:Class ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], + [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ] [ a owl:Restriction ; owl:onProperty biolink:has_attribute ; owl:someValuesFrom biolink:SocioeconomicAttribute ] ) ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; @@ -2396,11 +2397,11 @@ biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association ; linkml:attributes "{}" ; @@ -2416,13 +2417,13 @@ biolink:TextMiningResult a owl:Class ; biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Gene ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Transcript ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Gene ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is a collection of transcripts" ; linkml:attributes "{}" ; @@ -2463,6 +2464,14 @@ biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], @@ -2470,18 +2479,10 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], biolink:GeneExpressionMixin, biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" ; @@ -2493,40 +2494,40 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:VariantToEntityAssociationMixin ; @@ -2538,9 +2539,9 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; @@ -2548,23 +2549,23 @@ biolink:VariantToPopulationAssociation a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:onClass biolink:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PopulationOfIndividualOrganisms ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], biolink:Association, biolink:FrequencyQualifierMixin, biolink:FrequencyQuantifier, @@ -3471,10 +3472,6 @@ biolink:Article a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:issue ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:published_in ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -3483,6 +3480,10 @@ biolink:Article a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:published_in ; + owl:qualifiedCardinality 1 ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication " ; skos:exactMatch fabio:article, @@ -3519,14 +3520,14 @@ biolink:BookChapter a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:chapter ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:published_in ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:published_in ; + owl:qualifiedCardinality 1 ], biolink:Publication ; linkml:attributes "{}" ; linkml:is_a "publication" . @@ -3778,28 +3779,28 @@ biolink:GeneOrGeneProductOrChemicalEntityAspectEnum a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, @@ -3899,10 +3900,6 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ReactionSideEnum ; - owl:onProperty biolink:reaction_side ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:stoichiometry ], @@ -3914,6 +3911,10 @@ biolink:ReactionToParticipantAssociation a owl:Class ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ReactionSideEnum ; + owl:onProperty biolink:reaction_side ], biolink:ChemicalToChemicalAssociation ; linkml:attributes "{}" ; linkml:is_a "chemical to chemical association" . @@ -3947,6 +3948,9 @@ biolink:SymbolType a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Device ; + owl:onProperty biolink:has_device ], + [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], [ a owl:Restriction ; @@ -3956,9 +3960,6 @@ biolink:Treatment a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:Procedure ; owl:onProperty biolink:has_procedure ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Device ; - owl:onProperty biolink:has_device ], biolink:ChemicalOrDrugOrTreatment, biolink:ExposureEvent, biolink:NamedThing ; @@ -3976,25 +3977,25 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -5512,7 +5513,7 @@ biolink:latitude a owl:ObjectProperty ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:node_property ; skos:definition "latitude" ; - skos:exactMatch wgs:lat ; + skos:exactMatch wgs1:lat ; linkml:is_a "node property" . biolink:license a owl:ObjectProperty ; @@ -5538,7 +5539,7 @@ biolink:longitude a owl:ObjectProperty ; rdfs:range linkml:Float ; rdfs:subPropertyOf biolink:node_property ; skos:definition "longitude" ; - skos:exactMatch wgs:long ; + skos:exactMatch wgs1:long ; linkml:is_a "node property" . biolink:mapped_predicate a owl:ObjectProperty ; @@ -6355,12 +6356,12 @@ dct:distribution a owl:ObjectProperty ; skos:exactMatch dct:distribution ; linkml:is_a "node property" . -schema:logo a owl:ObjectProperty ; +schema1:logo a owl:ObjectProperty ; rdfs:label "source logo" ; rdfs:domain biolink:DatasetSummary ; rdfs:range linkml:String ; rdfs:subPropertyOf biolink:node_property ; - skos:exactMatch schema:logo ; + skos:exactMatch schema1:logo ; linkml:is_a "node property" . os:AllSomeInterpretation a owl:Class ; @@ -6758,21 +6759,21 @@ biolink:FDA_approval_status a owl:ObjectProperty ; biolink:FrequencyQuantifier a owl:Class ; rdfs:label "frequency quantifier" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], biolink:RelationshipQuantifier, linkml:mixin ; linkml:attributes "{}" ; @@ -6987,51 +6988,51 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onClass biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; @@ -7894,11 +7895,11 @@ biolink:DatasetSummary a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:source_web_page ], + owl:onProperty schema1:logo ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty schema:logo ], + owl:onProperty biolink:source_web_page ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." ; linkml:attributes "{}" ; @@ -7955,20 +7956,20 @@ biolink:GeneExpressionMixin a owl:Class ; rdfs:label "gene expression mixin" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], linkml:mixin ; skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; linkml:attributes "{}" . @@ -8058,30 +8059,19 @@ biolink:PredicateMapping a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; @@ -8089,53 +8079,64 @@ biolink:PredicateMapping a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:broad_match ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:mapped_predicate ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_aspect_qualifier ] ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:broad_match ] ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; linkml:attributes "{}" . @@ -8161,11 +8162,11 @@ biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; @@ -8410,13 +8411,13 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Dataset ; - owl:onProperty dct:source ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DatasetDistribution ; owl:onProperty dct:distribution ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Dataset ; + owl:onProperty dct:source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -8481,13 +8482,13 @@ biolink:PhysicalEntity a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Unit ; - owl:onProperty biolink:has_unit ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_numeric_value ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Unit ; + owl:onProperty biolink:has_unit ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; linkml:attributes "{}" ; @@ -8823,8 +8824,8 @@ biolink:Dataset a owl:Class ; rdfs:subClassOf biolink:InformationContentEntity ; skos:definition "an item that refers to a collection of data from a data source." ; skos:exactMatch IAO:0000100, - , - schema:dataset, + dcmitype:Dataset, + schema1:dataset, dcid:Dataset ; linkml:attributes "{}" ; linkml:is_a "information content entity" . @@ -8832,13 +8833,13 @@ biolink:Dataset a owl:Class ; biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:Disease ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:Disease ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:EntityToDiseaseAssociationMixin, biolink:GeneToDiseaseOrPhenotypicFeatureAssociation, biolink:GeneToEntityAssociationMixin ; @@ -8861,11 +8862,11 @@ biolink:LifeStage a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_input ], - [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_output ], @@ -9049,13 +9050,6 @@ rdf:type a owl:ObjectProperty ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalMixture ; - owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:highest_FDA_approval_status ], @@ -9063,6 +9057,13 @@ biolink:ChemicalMixture a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:drug_regulatory_status_world_wide ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:ChemicalMixture ; + owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; + owl:onProperty biolink:routes_of_delivery ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -9425,41 +9426,41 @@ biolink:Entity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CategoryType ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:NarrativeText ; - owl:onProperty dct:description ], + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:IriType ; owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:allValuesFrom biolink:Attribute ; - owl:onProperty biolink:has_attribute ] ; + owl:onProperty biolink:has_attribute ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CategoryType ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:NarrativeText ; + owl:onProperty dct:description ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ] ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; linkml:attributes "{}" . biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:Zygosity ; + owl:onProperty biolink:has_zygosity ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -9609,27 +9610,27 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:onClass biolink:PhenotypicFeature ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], biolink:EntityToFeatureOrDiseaseQualifiersMixin, biolink:FrequencyQuantifier, linkml:mixin ; @@ -9759,37 +9760,37 @@ biolink:Drug a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:PhaseEnum ; - owl:onProperty biolink:phase ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:end_interbase_coordinate ], + [ a owl:Restriction ; + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:StrandEnum ; owl:onProperty biolink:genome_build ], + [ a owl:Restriction ; + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:StrandEnum ; owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:start_interbase_coordinate ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:onClass biolink:PhaseEnum ; + owl:onProperty biolink:phase ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -9940,12 +9941,12 @@ biolink:EntityToDiseaseAssociationMixin a owl:Class ; biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSequence ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], biolink:GenomicEntity, biolink:MolecularEntity, biolink:OntologyClass, @@ -10030,20 +10031,20 @@ biolink:timepoint a owl:ObjectProperty ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:affiliation ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:address ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:affiliation ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -10061,14 +10062,14 @@ biolink:Agent a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:has_output ], - [ a owl:Restriction ; owl:allValuesFrom biolink:PhysicalEntity ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:has_output ], biolink:BiologicalEntity, biolink:Occurrent, biolink:OntologyClass ; @@ -10165,11 +10166,11 @@ biolink:InformationContentEntity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:rights ], + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:license ], + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Date ; @@ -10219,20 +10220,20 @@ biolink:OrganismTaxon a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:NamedThing ; owl:onProperty biolink:has_qualitative_value ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], biolink:NamedThing, biolink:OntologyClass ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; @@ -10319,13 +10320,12 @@ biolink:SequenceVariant a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:keywords ], [ a owl:Restriction ; owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:authors ], @@ -10333,12 +10333,13 @@ biolink:Publication a owl:Class ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:pages ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:keywords ], - [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:summary ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty biolink:mesh_terms ], @@ -10360,19 +10361,19 @@ biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty biolink:trade_name ], + owl:onClass linkml:Boolean ; + owl:onProperty biolink:is_toxic ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalRole ; + owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:max_tolerated_dose ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalRole ; - owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:is_toxic ], + owl:onClass biolink:ChemicalEntity ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:allValuesFrom biolink:DrugAvailabilityEnum ; owl:onProperty biolink:available_from ], @@ -10487,7 +10488,7 @@ biolink:OntologyClass a owl:Class ; owl:qualifiedCardinality 1 ], linkml:mixin ; skos:definition "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; - skos:exactMatch schema:Class, + skos:exactMatch schema1:Class, owl:Class ; linkml:attributes "{}" . @@ -10543,100 +10544,100 @@ biolink:related_to_at_instance_level a owl:ObjectProperty, biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:CategoryType ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:knowledge_source ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onClass linkml:Boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty biolink:object_closure ], + owl:onProperty rdf:type ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:subject_closure ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:object_category ], + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:subject_label_closure ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:subject_category ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:original_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:subject_closure ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:onClass linkml:String ; + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:allValuesFrom biolink:CategoryType ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:negated ], + owl:onClass linkml:String ; + owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:object_category ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -10648,8 +10649,8 @@ biolink:Association a owl:Class ; biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:provided_by ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:xref ], [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:CategoryType ; @@ -10657,8 +10658,8 @@ biolink:NamedThing a owl:Class ; owl:onProperty biolink:category ; owl:someValuesFrom biolink:CategoryType ] ) ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:xref ], + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:provided_by ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; skos:exactMatch STY:T071, diff --git a/biolink-model.shacl.ttl b/biolink-model.shacl.ttl index 4e090ff7c4..0de422e9b0 100644 --- a/biolink-model.shacl.ttl +++ b/biolink-model.shacl.ttl @@ -5,7 +5,7 @@ @prefix pav: . @prefix rdf: . @prefix rdfs: . -@prefix schema: . +@prefix schema1: . @prefix sh: . @prefix xsd: . @@ -13,16 +13,45 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; @@ -30,56 +59,41 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:AccessibleDnaRegion . + +biolink:Activity a sh:NodeShape ; + sh:closed true ; + sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 6 ; + sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ] ; - sh:targetClass biolink:AccessibleDnaRegion . - -biolink:Activity a sh:NodeShape ; - sh:closed true ; - sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:order 5 ; sh:path rdf:type ], [ sh:class biolink:Attribute ; @@ -89,21 +103,7 @@ biolink:Activity a sh:NodeShape ; sh:path biolink:has_attribute ], [ sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ] ; + sh:path biolink:description ] ; sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; @@ -115,19 +115,13 @@ biolink:ActivityAndBehavior a sh:NodeShape ; biolink:AdministrativeEntity a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -137,87 +131,34 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; + [ sh:order 5 ; + sh:path rdf:type ] ; sh:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:property [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -232,10 +173,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], [ sh:class biolink:AnatomicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -243,190 +180,252 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 21 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; @@ -434,43 +433,83 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at a later time" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ] ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the whole" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -478,102 +517,65 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the whole" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:AnatomicalEntity ; sh:description "the part" ; sh:maxCount 1 ; @@ -581,24 +583,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ] ; + sh:order 10 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . biolink:Annotation a sh:NodeShape ; @@ -611,83 +611,48 @@ biolink:Article a sh:NodeShape ; sh:closed true ; sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication " ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:description ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:has_attribute ], - [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:issue ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:order 18 ; - sh:path rdf:type ], - [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 9 ; sh:path biolink:xref ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:description "keywords tagging a publication" ; + sh:order 7 ; + sh:path biolink:keywords ], + [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:volume ], [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], + sh:order 11 ; + sh:path biolink:rights ], [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:license ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 14 ; sh:path biolink:provided_by ], - [ sh:description "keywords tagging a publication" ; - sh:order 7 ; - sh:path biolink:keywords ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:iri ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + sh:path biolink:mesh_terms ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -696,63 +661,60 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 17 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; - sh:targetClass biolink:Article . - -biolink:Association a sh:NodeShape ; - sh:closed true ; - sh:description "A typed association between two entities, supported by evidence" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:issue ], [ sh:maxCount 1 ; - sh:order 30 ; + sh:order 20 ; sh:path biolink:description ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 21 ; + sh:path biolink:has_attribute ], + [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 6 ; + sh:path biolink:summary ], + [ sh:order 18 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Article . + +biolink:Association a sh:NodeShape ; + sh:closed true ; + sh:description "A typed association between two entities, supported by evidence" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], @@ -764,16 +726,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 27 ; sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -781,89 +758,114 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ] ; sh:targetClass biolink:Association . biolink:Bacterium a sh:NodeShape ; sh:closed true ; sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -873,100 +875,93 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:order 6 ; - sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:Bacterium . - -biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; - sh:closed true ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:order 6 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Bacterium . + +biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; + sh:closed true ; sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:frequency_qualifier ], - [ sh:description "total number of things in a particular reference set" ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 21 ; + sh:path biolink:subject_namespace ], [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -974,16 +969,81 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 28 ; sh:path biolink:category ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:severity_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:BehavioralFeature ; sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; @@ -991,162 +1051,102 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], + sh:order 30 ; + sh:path rdfs:label ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_subject ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 34 ; + sh:path biolink:has_total ] ; + sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . + +biolink:BehavioralExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 0 ; sh:path biolink:timepoint ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . - -biolink:BehavioralExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ] ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ] ; sh:targetClass biolink:BehavioralExposure . biolink:BehavioralOutcome a sh:NodeShape ; @@ -1158,17 +1158,21 @@ biolink:BehavioralOutcome a sh:NodeShape ; biolink:BiologicalEntity a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1182,11 +1186,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], @@ -1194,68 +1198,42 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:order 6 ; - sh:path rdf:type ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ] ; sh:targetClass biolink:BiologicalEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:closed true ; sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_output ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_input ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:enabled_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1264,35 +1242,45 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_output ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ] ; sh:targetClass biolink:BiologicalProcessOrActivity . biolink:BioticExposure a sh:NodeShape ; sh:closed true ; sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a point in time" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1302,99 +1290,80 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:order 10 ; - sh:path rdf:type ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:has_qualitative_value ] ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:BioticExposure . biolink:Book a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Should generally be set to an ontology class defined term for 'book'." ; - sh:order 14 ; - sh:path rdf:type ], + sh:property [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], [ sh:description "keywords tagging a publication" ; sh:order 3 ; sh:path biolink:keywords ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "Books should have industry-standard identifier such as from ISBN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:order 14 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1404,39 +1373,74 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:creation_date ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:order 1 ; - sh:path biolink:pages ] ; + sh:path biolink:pages ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], + [ sh:description "Books should have industry-standard identifier such as from ISBN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ] ; sh:targetClass biolink:Book . biolink:BookChapter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:property [ sh:description "chapter of a book" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:chapter ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 13 ; + sh:path biolink:provided_by ], + [ sh:order 17 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:description ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:creation_date ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:published_in ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:description "chapter of a book" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:chapter ], - [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:volume ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1446,54 +1450,50 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 16 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 13 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:license ], - [ sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], [ sh:description "mesh terms tagging a publication" ; sh:order 7 ; sh:path biolink:mesh_terms ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:description ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:format ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], - [ sh:order 17 ; - sh:path rdf:type ], [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 18 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 8 ; sh:path biolink:xref ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:license ], [ sh:maxCount 1 ; sh:order 10 ; sh:path biolink:rights ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:creation_date ] ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:description "keywords tagging a publication" ; + sh:order 6 ; + sh:path biolink:keywords ], + [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:volume ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:BookChapter . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; @@ -1506,345 +1506,362 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:description "a point in time" ; + sh:property [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 29 ; sh:path rdf:type ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 36 ; + sh:path biolink:has_percentage ], [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 34 ; sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . - -biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 6 ; sh:path biolink:publications ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "number of things with a particular property" ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_count ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:order 38 ; + sh:path biolink:onset_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:path biolink:subject_closure ], [ sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 30 ; + sh:order 28 ; sh:path biolink:category ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:onset_qualifier ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], - [ sh:description "total number of things in a particular reference set" ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_total ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ] ; + sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . + +biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:severity_qualifier ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_count ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 29 ; sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], + sh:order 38 ; + sh:path biolink:has_percentage ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -1855,43 +1872,50 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 34 ; sh:path biolink:has_attribute ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:sex_qualifier ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ] ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ] ; sh:targetClass biolink:CausalGeneToDiseaseAssociation . biolink:Cell a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -1901,70 +1925,68 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], [ sh:order 6 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ] ; + sh:path rdf:type ] ; sh:targetClass biolink:Cell . biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 33 ; + sh:path biolink:onset_qualifier ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; @@ -1974,63 +1996,23 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -2038,14 +2020,14 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2053,193 +2035,211 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . - -biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:has_evidence ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:path biolink:id ] ; + sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + +biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ] ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; @@ -2252,7 +2252,14 @@ biolink:CellularOrganism a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -2261,14 +2268,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:order 6 ; sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -2277,69 +2285,43 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ] ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:CellularOrganism . biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 44 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:object_category_closure ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:order 14 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:iri ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:original_subject ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2347,171 +2329,258 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 40 ; sh:path biolink:category ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:object_namespace ], + [ sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_closure ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:object_label_closure ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:subject_namespace ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 25 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], + sh:order 24 ; + sh:path biolink:original_subject ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path rdfs:label ], + [ sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:subject_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 15 ; - sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 35 ; - sh:path biolink:subject_label_closure ], + sh:order 31 ; + sh:path biolink:subject_category_closure ], [ sh:maxCount 1 ; sh:order 43 ; sh:path biolink:description ], [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 41 ; + sh:path rdf:type ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 15 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 38 ; sh:path biolink:id ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:object_namespace ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:order 11 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 26 ; + sh:path biolink:original_object ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_evidence ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 41 ; - sh:path rdf:type ], - [ sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 18 ; + sh:path biolink:publications ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 36 ; - sh:path biolink:object_label_closure ], + sh:order 16 ; + sh:path biolink:negated ], [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 22 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:subject_label_closure ], [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; + sh:order 33 ; + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . + +biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; - sh:path biolink:subject_category_closure ], + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path rdfs:label ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 22 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; + sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2519,289 +2588,220 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "a point in time" ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 29 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . + +biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A regulatory relationship between two genes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:maxCount 1 ; - sh:order 30 ; + sh:order 31 ; sh:path biolink:description ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:ChemicalEntity ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; sh:path rdf:subject ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 16 ; - sh:path biolink:subject_closure ], + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 5 ; sh:path biolink:qualifiers ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "the direction is always from regulator to regulated" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:path biolink:subject_label_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; + sh:order 30 ; sh:path rdfs:label ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . - -biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A regulatory relationship between two genes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], + sh:order 19 ; + sh:path biolink:subject_category_closure ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "the direction is always from regulator to regulated" ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:order 12 ; + sh:path biolink:original_subject ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_predicate ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ] ; + sh:order 27 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; @@ -2820,33 +2820,17 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A chemical exposure is an intake of a particular chemical entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 2 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2856,15 +2840,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -2872,57 +2865,126 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_attribute_type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:timepoint ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:ChemicalExposure . biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:closed true ; sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:subject ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:subject_context_qualifier ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:object_part_qualifier ], - [ sh:class biolink:AnatomicalEntity ; + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:maxCount 1 ; sh:order 38 ; sh:path biolink:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path rdf:predicate ], + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 36 ; sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:qualifiers ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:original_subject ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2930,95 +2992,36 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 35 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "a point in time" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], [ sh:in ( "metabolite" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_derivative_qualifier ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:publications ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 17 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 14 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path rdf:predicate ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -3026,45 +3029,42 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 10 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:subject ], + sh:order 23 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ] ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:ChemicalGeneInteractionAssociation . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; @@ -3079,30 +3079,49 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:subject_namespace ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], + sh:order 16 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; @@ -3112,95 +3131,112 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path rdf:object ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + +biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -3208,58 +3244,50 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path rdf:subject ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], + sh:order 20 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:object_category ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 24 ; sh:path biolink:object_label_closure ], @@ -3268,85 +3296,77 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:subject_category ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], + sh:order 14 ; + sh:path biolink:original_object ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3354,99 +3374,94 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 28 ; sh:path biolink:category ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -3454,39 +3469,23 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3494,39 +3493,40 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 4 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:ChemicalToChemicalAssociation . biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; @@ -3540,75 +3540,108 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; THEN C1 derives-into C2 <>""" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:maxCount 1 ; sh:order 31 ; sh:path biolink:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 27 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], + sh:order 14 ; + sh:path biolink:original_object ], [ sh:class biolink:ChemicalEntity ; sh:description "the downstream chemical entity" ; sh:maxCount 1 ; @@ -3616,49 +3649,18 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:object_category ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path biolink:catalyst_qualifier ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], [ sh:class biolink:ChemicalEntity ; sh:description "the upstream chemical entity" ; sh:maxCount 1 ; @@ -3666,82 +3668,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; - sh:path biolink:original_subject ] ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; + sh:property [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; @@ -3754,36 +3711,77 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3792,51 +3790,53 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 27 ; sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ] ; + sh:order 4 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; @@ -3849,117 +3849,75 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that is affected by the chemical" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical entity that is affecting the pathway" ; sh:maxCount 1 ; @@ -3971,60 +3929,88 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ] ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:ChemicalToPathwayAssociation . biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -4037,6 +4023,23 @@ biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:path biolink:has_attribute ], [ sh:order 9 ; sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4045,24 +4048,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:ChiSquaredAnalysisResult . biolink:ClinicalCourse a sh:NodeShape ; sh:closed true ; sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -4081,14 +4074,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:maxCount 1 ; sh:order 10 ; sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], @@ -4097,15 +4082,30 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; @@ -4117,18 +4117,13 @@ biolink:ClinicalEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4138,161 +4133,158 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 5 ; - sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ] ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ClinicalEntity . biolink:ClinicalFinding a sh:NodeShape ; sh:closed true ; sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], [ sh:class biolink:ClinicalAttribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ClinicalFinding . - -biolink:ClinicalIntervention a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 4 ; + sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ClinicalIntervention . + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ] ; + sh:targetClass biolink:ClinicalFinding . -biolink:ClinicalMeasurement a sh:NodeShape ; +biolink:ClinicalIntervention a sh:NodeShape ; sh:closed true ; - sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; + sh:order 2 ; sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; + sh:order 3 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:order 5 ; + sh:path rdf:type ] ; + sh:targetClass biolink:ClinicalIntervention . + +biolink:ClinicalMeasurement a sh:NodeShape ; + sh:closed true ; + sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4302,61 +4294,55 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ClinicalMeasurement . biolink:ClinicalModifier a sh:NodeShape ; sh:closed true ; sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:order 9 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4366,31 +4352,33 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ] ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:ClinicalModifier . biolink:ClinicalTrial a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4400,26 +4388,43 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:order 5 ; - sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:order 5 ; + sh:path rdf:type ] ; sh:targetClass biolink:ClinicalTrial . biolink:CodingSequence a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -4428,90 +4433,73 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 12 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:order 13 ; + sh:path rdf:type ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:is_metabolite ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; sh:path biolink:provided_by ], - [ sh:order 13 ; - sh:path rdf:type ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], - [ sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:description ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ] ; + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ] ; sh:targetClass biolink:CodingSequence . biolink:Cohort a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; @@ -4525,60 +4513,78 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:order 6 ; sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ] ; sh:targetClass biolink:Cohort . biolink:CommonDataElement a sh:NodeShape ; sh:closed true ; sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4588,50 +4594,38 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:CommonDataElement . biolink:ComplexChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4641,24 +4635,30 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:order 9 ; sh:path rdf:type ] ; sh:targetClass biolink:ComplexChemicalExposure . @@ -4667,25 +4667,15 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4695,38 +4685,50 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalMixture ; + sh:description "" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:order 14 ; sh:path rdf:type ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; @@ -4736,58 +4738,48 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:class biolink:ChemicalMixture ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; - sh:path biolink:routes_of_delivery ] ; + sh:path biolink:routes_of_delivery ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ] ; sh:targetClass biolink:ComplexMolecularMixture . biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:property [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path biolink:description ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4797,12 +4789,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:ConceptCountAnalysisResult . biolink:ConfidenceLevel a sh:NodeShape ; @@ -4810,32 +4810,8 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:description "Level of confidence in a statement" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4845,69 +4821,62 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ] ; + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ] ; sh:targetClass biolink:ConfidenceLevel . biolink:ContributorAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 25 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4915,34 +4884,37 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:InformationContentEntity ; + sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:Agent ; sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; @@ -4950,240 +4922,117 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:InformationContentEntity ; - sh:description "information content entity which an agent has helped realise" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:ContributorAssociation . - -biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; - sh:path biolink:iri ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:path rdfs:label ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:frequency_qualifier ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 34 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:has_percentage ], - [ sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:onset_qualifier ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; - sh:path biolink:object_closure ], + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:sex_qualifier ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], + sh:order 5 ; + sh:path biolink:publications ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "total number of things in a particular reference set" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_total ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 6 ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 30 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:ContributorAssociation . + +biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:severity_qualifier ], + sh:order 40 ; + sh:path biolink:onset_qualifier ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_count ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_count ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is shown to correlate with the disease." ; sh:maxCount 1 ; @@ -5191,9 +5040,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path rdf:subject ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; @@ -5201,50 +5059,161 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 32 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . - -biolink:DatasetSummary a sh:NodeShape ; - sh:closed true ; - sh:description "an item that holds summary level information about a dataset." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:path rdfs:label ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 4 ; - sh:path biolink:format ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path rdf:predicate ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:rights ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:sex_qualifier ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:iri ], + sh:path biolink:has_evidence ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; + sh:order 28 ; sh:path biolink:id ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:source_web_page ], - [ sh:maxCount 1 ; - sh:order 13 ; + sh:order 33 ; sh:path biolink:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:publications ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . + +biolink:DatasetSummary a sh:NodeShape ; + sh:closed true ; + sh:description "an item that holds summary level information about a dataset." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:format ], [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:license ], + sh:order 0 ; + sh:path biolink:source_web_page ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5254,46 +5223,66 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 10 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:rights ], [ sh:maxCount 1 ; sh:order 1 ; - sh:path schema:logo ], + sh:path schema1:logo ], [ sh:order 11 ; sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:description ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:license ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ] ; sh:targetClass biolink:DatasetSummary . biolink:DatasetVersion a sh:NodeShape ; sh:closed true ; sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:rights ], - [ sh:order 12 ; - sh:path rdf:type ], + sh:property [ sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:format ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path pav:version ], - [ sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5303,55 +5292,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 11 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:DatasetDistribution ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:license ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:order 12 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:format ], + sh:order 1 ; + sh:path pav:version ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 9 ; sh:path biolink:id ], - [ sh:class biolink:Dataset ; + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:rights ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path dct:source ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:creation_date ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ] ; + [ sh:class biolink:DatasetDistribution ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path dct:distribution ], + [ sh:class biolink:Dataset ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path dct:source ], + [ sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:description ] ; sh:targetClass biolink:DatasetVersion . biolink:DiagnosticAid a sh:NodeShape ; sh:closed true ; sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5361,14 +5353,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; @@ -5378,73 +5362,89 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 3 ; sh:path biolink:iri ], [ sh:order 5 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ] ; sh:targetClass biolink:DiagnosticAid . biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:closed true ; sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 10 ; + sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; @@ -5462,13 +5462,20 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:closed true ; sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -5476,162 +5483,143 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:GeneticInheritance ; - sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:GeneticInheritance ; + sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; - sh:path biolink:object_closure ] ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -5639,76 +5627,108 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5716,44 +5736,24 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; @@ -5765,86 +5765,68 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an exposure event and a disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "a point in time" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:ExposureEvent ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -5852,18 +5834,30 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Disease ; sh:description "disease class" ; sh:maxCount 1 ; @@ -5871,198 +5865,156 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:DiseaseToExposureEventAssociation . - -biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 16 ; + sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 14 ; + sh:path biolink:subject_category ] ; + sh:targetClass biolink:DiseaseToExposureEventAssociation . + +biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], + sh:order 32 ; + sh:path biolink:has_attribute ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "number of things with a particular property" ; + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 29 ; sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:frequency_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 36 ; sh:path biolink:has_percentage ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; @@ -6071,52 +6023,107 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 27 ; sh:path biolink:iri ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 34 ; - sh:path biolink:has_total ] ; + sh:path biolink:has_total ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ] ; sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . biolink:DrugExposure a sh:NodeShape ; sh:closed true ; sh:description "A drug exposure is an intake of a particular drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 2 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -6126,57 +6133,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 1 ; sh:path biolink:has_quantitative_value ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], + [ sh:order 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:DrugExposure . biolink:DrugLabel a sh:NodeShape ; sh:closed true ; sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. " ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "executive summary of a publication" ; + sh:property [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -6186,55 +6194,47 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:creation_date ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:order 14 ; sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], [ sh:description "keywords tagging a publication" ; sh:order 3 ; sh:path biolink:keywords ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 16 ; - sh:path biolink:description ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ] ; + sh:path biolink:description ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; @@ -6247,95 +6247,101 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; @@ -6346,75 +6352,67 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product that is affected by the drug" ; + [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:DrugToGeneAssociation . + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ] ; + sh:targetClass biolink:DrugToGeneAssociation . biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:closed true ; sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 5 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 8 ; sh:path biolink:provided_by ], @@ -6432,245 +6430,236 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], - [ sh:order 11 ; - sh:path rdf:type ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_attribute_type ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; + sh:order 3 ; + sh:path rdfs:label ] ; sh:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "connects an association to an instance of supporting evidence" ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:publications ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], + sh:order 29 ; + sh:path biolink:iri ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 40 ; sh:path biolink:onset_qualifier ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:description ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_count ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:severity_qualifier ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], - [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 30 ; - sh:path biolink:category ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "total number of things in a particular reference set" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_total ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:sex_qualifier ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "connects an association to an instance of supporting evidence" ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:sex_qualifier ] ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_count ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ] ; sh:targetClass biolink:DruggableGeneToDiseaseAssociation . biolink:Entity a sh:NodeShape ; sh:closed false ; sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 2 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; @@ -6678,105 +6667,87 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:maxCount 1 ; sh:order 5 ; sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:iri ], [ sh:order 3 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_attribute ] ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 2 ; + sh:path biolink:category ] ; sh:targetClass biolink:Entity . biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_approval_status ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; @@ -6786,75 +6757,98 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 27 ; sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path rdf:predicate ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_approval_status ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_object ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:EntityToDiseaseAssociation . biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "mixin class for any association whose object (target node) is a disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:SeverityValue ; + sh:property [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -6863,7 +6857,13 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 2 ; - sh:path biolink:frequency_qualifier ] ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:onset_qualifier ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; @@ -6881,13 +6881,7 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for entity to disease or phenotype associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:onset_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:frequency_qualifier ], @@ -6896,7 +6890,13 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:severity_qualifier ] ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:onset_qualifier ] ; sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; @@ -6908,25 +6908,47 @@ biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_approval_status ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -6934,43 +6956,87 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:subject_category ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_approval_status ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -6978,170 +7044,67 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:maxCount 1 ; sh:order 31 ; - sh:path biolink:description ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ] ; + sh:path biolink:description ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:onset_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "total number of things in a particular reference set" ; + sh:property [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:has_total ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:severity_qualifier ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:onset_qualifier ], [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:has_percentage ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:has_count ] ; + sh:path biolink:has_count ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . biolink:EnvironmentalExposure a sh:NodeShape ; sh:closed true ; sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:maxCount 1 ; + sh:property [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -7153,48 +7116,77 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 1 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:EnvironmentalExposure . biolink:EnvironmentalFeature a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 5 ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:order 5 ; sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7204,6 +7196,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:description ] ; @@ -7212,15 +7212,27 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:order 4 ; + sh:path biolink:has_chemical_role ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7232,60 +7244,53 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:order 10 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 12 ; sh:path biolink:description ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ] ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:EnvironmentalFoodContaminant . biolink:EnvironmentalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7295,27 +7300,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:order 5 ; - sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; @@ -7337,13 +7337,22 @@ biolink:Event a sh:NodeShape ; sh:closed true ; sh:description "Something that happens at a given place and time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], @@ -7351,16 +7360,6 @@ biolink:Event a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7370,74 +7369,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ] ; + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Event . biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:closed true ; sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:Exon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:Transcript ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -7445,181 +7428,146 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Exon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ExonToTranscriptRelationship . - -biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an exposure event and an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 30 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 5 ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:population_context_qualifier ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:id ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ExonToTranscriptRelationship . + +biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between an exposure event and an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:subject_category ], + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:subject_namespace ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 29 ; - sh:path biolink:category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:object_closure ], - [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], + sh:order 23 ; + sh:path biolink:object_namespace ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category_closure ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -7629,32 +7577,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:maxCount 1 ; sh:order 32 ; sh:path biolink:description ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 0 ; + sh:path biolink:population_context_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:order 3 ; + sh:path rdf:predicate ], [ sh:class biolink:Outcome ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -7662,364 +7600,426 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 4 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path rdfs:label ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:timepoint ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 18 ; - sh:path biolink:subject_closure ] ; - sh:targetClass biolink:ExposureEventToOutcomeAssociation . - -biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:original_predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], + sh:order 5 ; + sh:path biolink:negated ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 30 ; + sh:order 31 ; sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 30 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 26 ; - sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_label_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; + sh:order 22 ; sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:path biolink:subject_category ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 29 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 33 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:object_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:order 28 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ExposureEventToOutcomeAssociation . + +biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:description "number of things with a particular property" ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 18 ; sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], + sh:order 1 ; + sh:path rdf:subject ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:frequency_qualifier ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ] ; - sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . - -biolink:Food a sh:NodeShape ; - sh:closed true ; - sh:description "A substance consumed by a living organism as a source of nutrition" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "" ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ] ; + sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . + +biolink:Food a sh:NodeShape ; + sh:closed true ; + sh:description "A substance consumed by a living organism as a source of nutrition" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:order 14 ; sh:path rdf:type ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:ChemicalMixture ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; - sh:path biolink:routes_of_delivery ] ; + sh:path biolink:routes_of_delivery ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:class biolink:ChemicalMixture ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:is_supplement ] ; sh:targetClass biolink:Food . biolink:FoodAdditive a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalRole ; + sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:description ], - [ sh:description "" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:order 10 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 1 ; sh:path biolink:available_from ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:trade_name ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ] ; + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:description ] ; sh:targetClass biolink:FoodAdditive . biolink:FrequencyQualifierMixin a sh:NodeShape ; @@ -8035,197 +8035,202 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; biolink:FrequencyQuantifier a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "number of things with a particular property" ; + sh:property [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_quotient ], + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_count ], - [ sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_total ], [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:has_percentage ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_quotient ] ; + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_total ] ; sh:targetClass biolink:FrequencyQuantifier . biolink:FunctionalAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:FunctionalAssociation . biolink:Fungus a sh:NodeShape ; sh:closed true ; sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 6 ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 6 ; sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; @@ -8235,219 +8240,220 @@ biolink:Fungus a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ] ; sh:targetClass biolink:Fungus . biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:id ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 38 ; sh:path biolink:has_percentage ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:iri ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:description "The relationship to the disease" ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:negated ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:sex_qualifier ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 30 ; - sh:path biolink:category ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 36 ; + sh:path biolink:has_total ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:severity_qualifier ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:frequency_qualifier ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:severity_qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ], [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 35 ; sh:path biolink:has_count ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:onset_qualifier ], - [ sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_total ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . biolink:GeneExpressionMixin a sh:NodeShape ; sh:closed false ; sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:class biolink:OntologyClass ; sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -8459,12 +8465,6 @@ biolink:GeneExpressionMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:phenotypic_state ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; @@ -8487,210 +8487,210 @@ biolink:GeneGroupingMixin a sh:NodeShape ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 30 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 31 ; + sh:path biolink:category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 29 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 41 ; sh:path biolink:onset_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:description ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:order 38 ; + sh:path biolink:has_quotient ], [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 36 ; sh:path biolink:has_count ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 31 ; - sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_total ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:id ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:has_quotient ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 32 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:frequency_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path rdfs:label ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 40 ; sh:path biolink:severity_qualifier ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 32 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:order 5 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_total ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 2 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path rdfs:label ], + sh:order 39 ; + sh:path biolink:has_percentage ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNode ; sh:order 4 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:description ] ; sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:closed false ; sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 2 ; sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ] ; @@ -8699,29 +8699,83 @@ biolink:GeneProductIsoformMixin a sh:NodeShape ; biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:property [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:onset_qualifier ], + sh:order 5 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:id ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:sex_qualifier ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; sh:maxCount 1 ; @@ -8729,340 +8783,242 @@ biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path rdf:subject ], - [ sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], + sh:order 32 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 30 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:sex_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 35 ; + sh:path biolink:has_count ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 36 ; sh:path biolink:has_total ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:severity_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:description ], + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 41 ; sh:path biolink:frequency_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:negated ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_count ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ] ; + sh:order 21 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:GeneToDiseaseAssociation . biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:id ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:sex_qualifier ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:onset_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_total ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:severity_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_count ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], + sh:order 2 ; + sh:path biolink:sex_qualifier ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9070,16 +9026,60 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 30 ; sh:path biolink:category ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:has_percentage ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ] ; + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_count ] ; sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . biolink:GeneToEntityAssociationMixin a sh:NodeShape ; @@ -9091,31 +9091,46 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:iri ], + sh:order 31 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:object_category ], + sh:order 16 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], + sh:order 20 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:negated ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; sh:maxCount 1 ; @@ -9123,19 +9138,6 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:object_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9143,219 +9145,170 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 29 ; sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_label_closure ], + [ sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_object ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 22 ; + sh:path biolink:subject_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 30 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 12 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_subject ], + sh:order 28 ; + sh:path biolink:iri ], [ sh:class biolink:LifeStage ; sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:stage_qualifier ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:object_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 30 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 15 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "can be used to indicate magnitude, or also ranking" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 1 ; + sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 33 ; + sh:path biolink:has_attribute ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "expression relationship" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:subject_namespace ], - [ sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:description ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; + sh:order 14 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_label_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 27 ; + sh:path biolink:id ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:subject_category ] ; + sh:order 6 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:GeneToExpressionSiteAssociation . biolink:GeneToGeneAssociation a sh:NodeShape ; sh:closed false ; sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; @@ -9367,18 +9320,21 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; @@ -9388,75 +9344,80 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ] ; - sh:targetClass biolink:GeneToGeneAssociation . - -biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 32 ; + sh:order 28 ; sh:path rdf:type ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:maxCount 1 ; + sh:path biolink:negated ] ; + sh:targetClass biolink:GeneToGeneAssociation . + +biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; sh:order 34 ; sh:path biolink:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 33 ; + sh:path rdfs:label ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -9464,75 +9425,27 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 6 ; sh:path rdf:object ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 29 ; - sh:path biolink:id ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -9540,11 +9453,42 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 4 ; sh:path rdf:subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:id ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path rdf:predicate ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9552,60 +9496,124 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 31 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 11 ; - sh:path biolink:knowledge_source ] ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:iri ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 32 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GeneToGeneCoexpressionAssociation . biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; sh:closed true ; sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "membership of the gene in the given gene family." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9613,132 +9621,128 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:GeneFamily ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "membership of the gene in the given gene family." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ] ; + sh:order 4 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:GeneToGeneFamilyAssociation . biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:closed true ; sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -9746,16 +9750,6 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -9763,15 +9757,6 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9779,113 +9764,124 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description "homology relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ] ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ] ; sh:targetClass biolink:GeneToGeneHomologyAssociation . biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:closed true ; sh:description "A gene is transcribed and potentially translated to a gene product" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:GeneProductMixin ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9893,50 +9889,45 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:Gene ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9944,50 +9935,64 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], @@ -9996,20 +10001,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -10020,191 +10020,190 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ] ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:GeneToGoTermAssociation . biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a gene or gene product and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "a point in time" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the gene or gene product entity that participates or influences the pathway" ; sh:maxCount 1 ; @@ -10212,61 +10211,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], [ sh:class biolink:Pathway ; sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; @@ -10274,117 +10234,118 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ] ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:GeneToPathwayAssociation . biolink:GeneToPhenotypeAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 32 ; sh:path rdfs:label ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "number of things with a particular property" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 35 ; sh:path biolink:has_count ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:order 36 ; + sh:path biolink:has_total ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:onset_qualifier ], + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:id ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; @@ -10392,132 +10353,175 @@ biolink:GeneToPhenotypeAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:iri ], + sh:order 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 30 ; - sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path rdf:predicate ], - [ sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:severity_qualifier ], + sh:order 29 ; + sh:path biolink:iri ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "total number of things in a particular reference set" ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "secretion" "uptake" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 31 ; sh:path rdf:type ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:has_percentage ] ; + sh:order 34 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GeneToPhenotypeAssociation . biolink:Genome a sh:NodeShape ; sh:closed true ; sh:description "A genome is the sum of genetic material within a cell or virion." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10527,56 +10531,71 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 4 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:path biolink:xref ] ; sh:targetClass biolink:Genome . biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:closed true ; sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:order 13 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 11 ; sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 13 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -10584,29 +10603,27 @@ biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_attribute_type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_qualitative_value ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 5 ; @@ -10616,28 +10633,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 7 ; sh:path biolink:has_quantitative_value ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:description ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_gene_or_gene_product ] ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; @@ -10653,209 +10653,209 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:closed true ; sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:description ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:order 0 ; + sh:path biolink:start_interbase_coordinate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:strand ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path rdf:predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - sh:in ( "+" "-" "." "?" ) ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:genome_build ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:description ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 27 ; sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; + [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; + sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:end_interbase_coordinate ], - [ sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:order 2 ; + sh:path biolink:genome_build ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 26 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:end_interbase_coordinate ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 32 ; + sh:path biolink:category ], [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; sh:in ( "0" "1" "2" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:phase ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ] ; + sh:order 23 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:GenomicSequenceLocalization . biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10863,136 +10863,101 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:onset_qualifier ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:frequency_qualifier ] ; - sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . - -biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; @@ -11006,45 +10971,56 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . + +biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11052,101 +11028,125 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 34 ; sh:path biolink:frequency_qualifier ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "E.g. is pathogenic for" ; + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:onset_qualifier ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that genotype" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ] ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:GenotypeToDiseaseAssociation . biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; @@ -11158,87 +11158,49 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], + sh:property [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Gene ; - sh:description "gene implicated in genotype" ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "a point in time" ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -11251,72 +11213,41 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "the relationship type used to connect genotype to gene" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ] ; - sh:targetClass biolink:GenotypeToGeneAssociation . - -biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -11324,61 +11255,86 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Genotype ; - sh:description "child genotype" ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:Gene ; + sh:description "gene implicated in genotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:GenotypeToGeneAssociation . + +biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Genotype ; + sh:description "child genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11386,173 +11342,170 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:GenotypeToGenotypePartAssociation . - -biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:path biolink:subject_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 32 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 8 ; + sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "total number of things in a particular reference set" ; + sh:path biolink:object_label_closure ] ; + sh:targetClass biolink:GenotypeToGenotypePartAssociation . + +biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:order 13 ; + sh:path biolink:original_predicate ], [ sh:maxCount 1 ; sh:order 35 ; sh:path biolink:has_quotient ], @@ -11561,23 +11514,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 29 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 3 ; + sh:path rdf:object ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], [ sh:class biolink:Genotype ; sh:description "genotype that is associated with the phenotypic feature" ; sh:maxCount 1 ; @@ -11585,92 +11534,125 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_subject ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:description "number of things with a particular property" ; + sh:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ] ; + sh:order 36 ; + sh:path biolink:has_percentage ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11678,14 +11660,23 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -11693,146 +11684,121 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "the relationship type used to connect genotype to gene" ; + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:maxCount 1 ; sh:order 30 ; - sh:path biolink:description ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ] ; + sh:path biolink:description ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:property [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11842,41 +11808,64 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:GenotypicSex . - -biolink:GeographicExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; + sh:order 4 ; sh:path biolink:iri ], - [ sh:description "a point in time" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:timepoint ], + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; + sh:order 7 ; sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ] ; + sh:targetClass biolink:GenotypicSex . + +biolink:GeographicExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -11888,71 +11877,71 @@ biolink:GeographicExposure a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:GeographicExposure . biolink:GeographicLocation a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "latitude" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:latitude ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "latitude" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "longitude" ; + sh:order 0 ; + sh:path biolink:latitude ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:longitude ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:order 7 ; sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], @@ -11964,20 +11953,33 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "longitude" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:longitude ] ; sh:targetClass biolink:GeographicLocation . biolink:GeographicLocationAtTime a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates, for a particular time" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:order 8 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; sh:order 10 ; sh:path biolink:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11987,59 +11989,61 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 7 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "latitude" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:latitude ], + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], [ sh:description "longitude" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:longitude ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "latitude" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:order 8 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:latitude ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:order 6 ; - sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12049,60 +12053,32 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:GrossAnatomicalStructure . biolink:Haplotype a sh:NodeShape ; sh:closed true ; sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:property [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12112,24 +12088,54 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ] ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Haplotype . biolink:Hospitalization a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -12140,20 +12146,6 @@ biolink:Hospitalization a sh:NodeShape ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12163,8 +12155,16 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 5 ; - sh:path rdf:type ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -12177,133 +12177,118 @@ biolink:Human a sh:NodeShape ; sh:closed true ; sh:description "A member of the the species Homo sapiens." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Human . biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:closed true ; sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "a point in time" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -12314,61 +12299,76 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ] ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . biolink:InformationResourceContainer a sh:NodeShape ; @@ -12386,22 +12386,24 @@ biolink:Invertebrate a sh:NodeShape ; sh:closed true ; sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12411,182 +12413,203 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ] ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Invertebrate . biolink:JournalArticle a sh:NodeShape ; sh:closed true ; sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], - [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:issue ], - [ sh:description "executive summary of a publication" ; + sh:property [ sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:description ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 14 ; sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:format ], [ sh:maxCount 1 ; sh:order 10 ; sh:path biolink:license ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 5 ; - sh:path biolink:pages ], [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:published_in ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], - [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + sh:path biolink:mesh_terms ], + [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:summary ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ], [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 19 ; sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ sh:order 18 ; sh:path rdf:type ], - [ sh:description "keywords tagging a publication" ; - sh:order 7 ; - sh:path biolink:keywords ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:iri ], [ sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:description ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ] ; + sh:order 11 ; + sh:path biolink:rights ], + [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:issue ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:volume ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:description "keywords tagging a publication" ; + sh:order 7 ; + sh:path biolink:keywords ] ; sh:targetClass biolink:JournalArticle . biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a log odds ratio analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:order 9 ; sh:path rdf:type ], [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 6 ; + sh:path biolink:id ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ] ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:order 7 ; + sh:path rdf:type ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 2 ; sh:path biolink:provided_by ], @@ -12603,41 +12626,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:MacromolecularComplex . biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; + sh:property [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:BiologicalProcess ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -12645,98 +12685,83 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "a point in time" ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:BiologicalProcess ; - sh:description "class describing the activity, process or localization of the gene product" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12744,128 +12769,83 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ] ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ] ; sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12873,24 +12853,6 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], [ sh:class biolink:CellularComponent ; sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; @@ -12898,6 +12860,32 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -12905,27 +12893,39 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ] ; + sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; @@ -12937,25 +12937,48 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12963,9 +12986,37 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], @@ -12975,71 +13026,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; @@ -13049,44 +13041,62 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ] ; sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . biolink:Mammal a sh:NodeShape ; sh:closed true ; sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -13095,9 +13105,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], @@ -13105,30 +13112,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Mammal . biolink:MappingCollection a sh:NodeShape ; @@ -13146,96 +13146,46 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; + [ sh:description "derivation relationship" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -13243,201 +13193,251 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "derivation relationship" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:NamedThing ; + sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; - sh:path biolink:timepoint ] ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ] ; sh:targetClass biolink:MaterialSampleDerivationAssociation . biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and a disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ] ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; @@ -13449,7 +13449,13 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:max_tolerated_dose ], @@ -13457,47 +13463,25 @@ biolink:MicroRNA a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:is_toxic ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_chemical_role ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 7 ; @@ -13508,24 +13492,40 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:trade_name ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:is_metabolite ] ; + sh:path biolink:is_metabolite ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; @@ -13538,99 +13538,109 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13638,10 +13648,23 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13649,56 +13672,27 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ] ; + sh:order 15 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; @@ -13707,81 +13701,92 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; @@ -13791,70 +13796,102 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ] ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13862,166 +13899,115 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ] ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:MolecularActivityToPathwayAssociation . biolink:MolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:property [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description "" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 15 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalEntity ; + [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14031,39 +14017,53 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:ChemicalMixture ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "" ; + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ] ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -14076,41 +14076,33 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14118,65 +14110,91 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -14191,48 +14209,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . biolink:NoncodingRNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:property [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:is_metabolite ], @@ -14240,17 +14232,6 @@ biolink:NoncodingRNAProduct a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:order 14 ; - sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], @@ -14260,26 +14241,38 @@ biolink:NoncodingRNAProduct a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:trade_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_chemical_role ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 7 ; sh:path biolink:available_from ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:is_toxic ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14289,51 +14282,41 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:has_biological_sequence ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ] ; + sh:order 10 ; + sh:path biolink:has_chemical_role ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:closed true ; sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:order 6 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14343,57 +14326,53 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:NucleicAcidSequenceMotif . - -biolink:NucleosomeModification a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; - sh:path biolink:provided_by ], + sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:NucleicAcidSequenceMotif . + +biolink:NucleosomeModification a sh:NodeShape ; + sh:closed true ; + sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 11 ; - sh:path biolink:synonym ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], [ sh:order 7 ; sh:path rdf:type ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14403,40 +14382,67 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ] ; + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 11 ; + sh:path biolink:synonym ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14447,22 +14453,16 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 0 ; + sh:path biolink:license ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; @@ -14475,23 +14475,43 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:closed true ; sh:description "describes a characteristic of an organismal entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14501,36 +14521,16 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:maxCount 1 ; sh:order 10 ; sh:path biolink:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:OrganismAttribute . biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; @@ -14542,101 +14542,75 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "the environment in which the organism occurs" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:NamedThing ; + sh:description "the environment in which the organism occurs" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -14644,133 +14618,155 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ] ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:closed false ; sh:description "A relationship between two organism taxon nodes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -14778,29 +14774,22 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OrganismTaxon ; sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -14808,259 +14797,231 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "a point in time" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ] ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "the environment in which the two taxa interact" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 14 ; + sh:path biolink:original_object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], + sh:order 0 ; + sh:path biolink:associated_environmental_context ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ] ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:closed true ; sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; @@ -15069,19 +15030,6 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OrganismTaxon ; sh:description "the more general taxon" ; sh:maxCount 1 ; @@ -15094,6 +15042,9 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15101,18 +15052,43 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; @@ -15122,51 +15098,98 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ] ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:IndividualOrganism ; sh:description "An association between two individual organisms." ; sh:maxCount 1 ; @@ -15174,143 +15197,107 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:IndividualOrganism ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ] ; + sh:path rdf:predicate ] ; sh:targetClass biolink:OrganismToOrganismAssociation . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; @@ -15319,94 +15306,115 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:severity_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OrganismalEntity ; sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; sh:maxCount 1 ; @@ -15414,68 +15422,54 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 33 ; + sh:path biolink:onset_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15483,35 +15477,74 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; @@ -15521,126 +15554,110 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; - sh:path biolink:subject_label_closure ] ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:PairwiseGeneToGeneInteraction . biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction at the molecular level between two physical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:MolecularEntity ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_subject ], + [ sh:description "interaction relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], [ sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 26 ; sh:path biolink:id ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:class biolink:MolecularEntity ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -15648,184 +15665,167 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:MolecularEntity ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], + sh:order 3 ; + sh:path rdf:object ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:timepoint ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], + sh:order 30 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], + sh:order 15 ; + sh:path biolink:subject_category ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 29 ; sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], [ sh:maxCount 1 ; sh:order 31 ; sh:path biolink:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:subject_namespace ], - [ sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], + sh:order 22 ; + sh:path biolink:object_namespace ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ] ; + sh:path biolink:negated ] ; sh:targetClass biolink:PairwiseMolecularInteraction . biolink:Patent a sh:NodeShape ; sh:closed true ; sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. " ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:property [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:creation_date ], - [ sh:description "executive summary of a publication" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 12 ; + sh:path biolink:iri ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:rights ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:format ], - [ sh:order 14 ; - sh:path rdf:type ], [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; sh:path biolink:mesh_terms ], + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ] ; + sh:order 16 ; + sh:path biolink:description ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -15838,30 +15838,7 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:closed true ; sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -15873,20 +15850,10 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; @@ -15896,53 +15863,54 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:order 10 ; - sh:path rdf:type ] ; - sh:targetClass biolink:PathologicalAnatomicalExposure . - -biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PathologicalAnatomicalOutcome . - -biolink:PathologicalAnatomicalStructure a sh:NodeShape ; - sh:closed true ; - sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; + sh:order 8 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:order 10 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; + sh:order 6 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:PathologicalAnatomicalExposure . + +biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PathologicalAnatomicalOutcome . + +biolink:PathologicalAnatomicalStructure a sh:NodeShape ; + sh:closed true ; + sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -15951,8 +15919,40 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:order 6 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PathologicalAnatomicalStructure . biolink:PathologicalEntityMixin a sh:NodeShape ; @@ -15965,74 +15965,94 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ] ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:PathologicalProcess . biolink:PathologicalProcessExposure a sh:NodeShape ; sh:closed true ; sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 1 ; + sh:path rdfs:label ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16042,24 +16062,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -16067,28 +16083,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -16101,9 +16101,30 @@ biolink:Phenomenon a sh:NodeShape ; sh:closed true ; sh:description "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16113,39 +16134,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Phenomenon . biolink:PhenotypicQuality a sh:NodeShape ; sh:closed true ; sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -16154,24 +16173,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -16179,81 +16185,61 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:order 9 ; - sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:PhenotypicQuality . biolink:PhenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16262,7 +16248,21 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; @@ -16280,45 +16280,40 @@ biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16328,38 +16323,34 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ] ; sh:targetClass biolink:PhysiologicalProcess . biolink:PlanetaryEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists at the level of the whole planet" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16369,38 +16360,39 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 5 ; - sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ] ; + [ sh:order 5 ; + sh:path rdf:type ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:order 6 ; - sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16410,13 +16402,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; @@ -16427,27 +16428,40 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Plant . biolink:Polypeptide a sh:NodeShape ; sh:closed true ; sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:order 6 ; sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16457,81 +16471,42 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ] ; sh:targetClass biolink:Polypeptide . biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a two populations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that form the object of the association" ; sh:maxCount 1 ; @@ -16544,115 +16519,123 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 11 ; + sh:path biolink:original_subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:PopulationToPopulationAssociation . biolink:PosttranslationalModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; @@ -16660,6 +16643,15 @@ biolink:PosttranslationalModification a sh:NodeShape ; [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16669,41 +16661,36 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:PosttranslationalModification . biolink:PreprintPublication a sh:NodeShape ; sh:closed true ; sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:creation_date ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16713,21 +16700,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], [ sh:description "keywords tagging a publication" ; sh:order 3 ; sh:path biolink:keywords ], @@ -16735,72 +16713,91 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:order 14 ; + sh:path rdf:type ], [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:rights ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:maxCount 1 ; sh:order 6 ; - sh:path biolink:license ] ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ] ; sh:targetClass biolink:PreprintPublication . biolink:ProcessedMaterial a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:ChemicalMixture ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:order 14 ; + sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 16 ; sh:path biolink:description ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:class biolink:ChemicalMixture ; - sh:description "" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; @@ -16809,19 +16806,6 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16837,23 +16821,44 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:trade_name ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ] ; sh:targetClass biolink:ProcessedMaterial . biolink:Protein a sh:NodeShape ; sh:closed true ; sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 7 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16863,26 +16868,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], @@ -16890,31 +16878,35 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Protein . - -biolink:ProteinDomain a sh:NodeShape ; - sh:closed true ; - sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:path biolink:id ] ; + sh:targetClass biolink:Protein . + +biolink:ProteinDomain a sh:NodeShape ; + sh:closed true ; + sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16924,9 +16916,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; @@ -16937,47 +16938,47 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:order 7 ; - sh:path rdf:type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:ProteinDomain . biolink:ProteinFamily a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:order 7 ; - sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 9 ; sh:path biolink:description ], @@ -16990,35 +16991,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:order 1 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:ProteinFamily . biolink:ProteinIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; @@ -17028,55 +17016,67 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; - sh:path biolink:synonym ] ; + sh:path biolink:synonym ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:ProteinIsoform . biolink:RNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:property [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:trade_name ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:description "" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 9 ; + sh:path biolink:is_toxic ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17086,133 +17086,133 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_chemical_role ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:trade_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 7 ; - sh:path biolink:available_from ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:is_metabolite ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:RNAProduct . - -biolink:RNAProductIsoform a sh:NodeShape ; - sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:path biolink:synonym ], [ sh:order 14 ; sh:path rdf:type ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_chemical_role ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 7 ; + sh:path biolink:available_from ] ; + sh:targetClass biolink:RNAProduct . + +biolink:RNAProductIsoform a sh:NodeShape ; + sh:closed true ; + sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:trade_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:is_toxic ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:is_metabolite ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:trade_name ], + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 7 ; sh:path biolink:available_from ], - [ sh:description "" ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_chemical_role ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:is_toxic ], + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 15 ; @@ -17222,184 +17222,64 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], [ sh:maxCount 1 ; sh:order 33 ; sh:path biolink:description ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:iri ], [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 8 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 30 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:id ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 20 ; sh:path biolink:object_closure ], @@ -17408,32 +17288,55 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 4 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17441,35 +17344,53 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 30 ; sh:path biolink:category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the chemical element that is the target of the statement" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 5 ; + sh:path rdf:object ], [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:stoichiometry ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 21 ; + sh:path biolink:subject_category_closure ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:MolecularEntity ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -17477,22 +17398,85 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:subject ], - [ sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:description ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 28 ; sh:path biolink:id ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -17500,129 +17484,142 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 5 ; sh:path rdf:object ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 32 ; sh:path rdfs:label ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 30 ; + sh:path biolink:category ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], + sh:minCount 1 ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 31 ; sh:path rdf:type ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:reaction_direction ], - [ sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ] ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; sh:closed true ; sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:id ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:maxCount 1 ; sh:order 9 ; sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 3 ; sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ] ; + sh:order 8 ; + sh:path rdfs:label ] ; sh:targetClass biolink:ReagentTargetedGene . biolink:RegulatoryRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17632,21 +17629,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 6 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:order 7 ; sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ] ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:RegulatoryRegion . biolink:RelationshipQuantifier a sh:NodeShape ; @@ -17669,7 +17669,11 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a relative frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -17678,120 +17682,56 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ] ; - sh:targetClass biolink:RelativeFrequencyAnalysisResult . - -biolink:SensitivityQuantifier a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SensitivityQuantifier . - -biolink:SequenceAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; + sh:order 10 ; sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:RelativeFrequencyAnalysisResult . + +biolink:SensitivityQuantifier a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SensitivityQuantifier . + +biolink:SequenceAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; @@ -17801,40 +17741,51 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -17842,84 +17793,44 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 16 ; sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ] ; - sh:targetClass biolink:SequenceAssociation . - -biolink:SequenceFeatureRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "For example, a particular exon is part of a particular transcript or gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17927,23 +17838,103 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:SequenceAssociation . + +biolink:SequenceFeatureRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "For example, a particular exon is part of a particular transcript or gene" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:maxCount 1 ; sh:order 30 ; sh:path biolink:description ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; @@ -17954,35 +17945,38 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:NucleicAcidEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -17990,227 +17984,270 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ] ; + sh:order 10 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:SequenceFeatureRelationship . biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:closed false ; sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; + sh:property [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; sh:path biolink:subject_label_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 25 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ] ; + sh:path biolink:category ] ; sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . biolink:Serial a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:format ], + sh:property [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:issue ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 13 ; + sh:path biolink:provided_by ], [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:order 18 ; sh:path rdfs:label ], - [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:issue ], + sh:order 15 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + sh:path biolink:mesh_terms ], + [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:volume ], + [ sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:description ], + [ sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:iso_abbreviation ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:format ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:creation_date ], - [ sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], [ sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:id ], [ sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path biolink:license ], + [ sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 7 ; - sh:path biolink:mesh_terms ], + sh:order 5 ; + sh:path biolink:summary ], + [ sh:description "keywords tagging a publication" ; + sh:order 6 ; + sh:path biolink:keywords ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:rights ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18220,129 +18257,92 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 16 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:volume ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:order 4 ; - sh:path biolink:pages ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:rights ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 13 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:license ] ; + sh:path biolink:pages ] ; sh:targetClass biolink:Serial . biolink:SiRNA a sh:NodeShape ; sh:closed true ; sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], - [ sh:order 14 ; - sh:path rdf:type ], + sh:property [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:is_metabolite ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:trade_name ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], [ sh:description "" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:is_toxic ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 7 ; - sh:path biolink:available_from ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_chemical_role ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_chemical_role ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:order 8 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 7 ; + sh:path biolink:available_from ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:is_metabolite ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:trade_name ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + [ sh:order 14 ; + sh:path rdf:type ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; @@ -18353,37 +18353,37 @@ biolink:SmallMolecule a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "" ; + [ sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18393,55 +18393,64 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 10 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:is_toxic ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:order 11 ; sh:path rdf:type ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:trade_name ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ] ; + sh:path biolink:trade_name ] ; sh:targetClass biolink:SmallMolecule . biolink:Snv a sh:NodeShape ; sh:closed true ; sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "The state of the sequence w.r.t a reference sequence" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ], + [ sh:order 8 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18454,31 +18463,46 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:order 8 ; - sh:path rdf:type ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; + [ sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ] ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Snv . biolink:SocioeconomicExposure a sh:NodeShape ; sh:closed true ; sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:SocioeconomicAttribute ; + sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -18495,12 +18519,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:order 10 ; sh:path rdf:type ], - [ sh:class biolink:SocioeconomicAttribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -18512,33 +18538,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ] ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:SocioeconomicExposure . biolink:SocioeconomicOutcome a sh:NodeShape ; @@ -18556,57 +18556,59 @@ biolink:Study a sh:NodeShape ; sh:closed true ; sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Study . biolink:StudyPopulation a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group as participants in a research study." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:order 6 ; + sh:property [ sh:order 6 ; sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18616,129 +18618,133 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:StudyPopulation . biolink:StudyResult a sh:NodeShape ; sh:closed false ; sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:property [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], + sh:order 0 ; + sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ] ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:StudyResult . biolink:StudyVariable a sh:NodeShape ; sh:closed true ; sh:description "a variable that is used as a measure in the investigation of a study" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18749,14 +18755,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:order 1 ; + sh:path biolink:rights ] ; sh:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; @@ -18768,31 +18768,23 @@ biolink:SubjectOfInvestigation a sh:NodeShape ; biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 5 ; + sh:path biolink:publications ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -18800,6 +18792,16 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -18807,30 +18809,27 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18838,79 +18837,80 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ] ; + sh:path biolink:object_category ] ; sh:targetClass biolink:TaxonToTaxonAssociation . biolink:TaxonomicRank a sh:NodeShape ; @@ -18928,32 +18928,33 @@ biolink:TextMiningResult a sh:NodeShape ; sh:closed true ; sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; @@ -18963,22 +18964,21 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 2 ; - sh:path biolink:format ] ; + sh:path biolink:format ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ] ; sh:targetClass biolink:TextMiningResult . biolink:ThingWithTaxon a sh:NodeShape ; @@ -18996,57 +18996,83 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:closed true ; sh:description "A gene is a collection of transcripts" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:Transcript ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -19054,240 +19080,234 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 26 ; + sh:path biolink:iri ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + sh:order 21 ; + sh:path biolink:object_namespace ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 17 ; sh:path biolink:object_closure ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ] ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:TranscriptToGeneRelationship . biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:order 7 ; - sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:TranscriptionFactorBindingSite . biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:property [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 5 ; + sh:path biolink:publications ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:original_predicate ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "The relationship to the disease" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 34 ; sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 33 ; + sh:path biolink:onset_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category_closure ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -19295,97 +19315,138 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 27 ; sh:path biolink:category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:class biolink:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:severity_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path biolink:publications ], + [ sh:description "E.g. is pathogenic for" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; sh:maxCount 1 ; @@ -19393,70 +19454,35 @@ biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:description "E.g. is pathogenic for" ; + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description "a point in time" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 12 ; + sh:path biolink:original_predicate ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 7 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path biolink:object_category ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; @@ -19467,59 +19493,33 @@ biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 4 ; + sh:path biolink:qualifiers ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 34 ; sh:path biolink:frequency_qualifier ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ] ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:VariantToDiseaseAssociation . biolink:VariantToEntityAssociationMixin a sh:NodeShape ; @@ -19531,73 +19531,97 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 27 ; + sh:path biolink:category ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:subject_closure ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 9 ; - sh:path biolink:aggregator_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], - [ sh:description "a point in time" ; + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:iri ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 20 ; sh:path biolink:subject_namespace ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:object_closure ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 16 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 9 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_label_closure ], [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 12 ; @@ -19606,129 +19630,135 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 21 ; sh:path biolink:object_namespace ], - [ sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 5 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 27 ; - sh:path biolink:category ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:object_category ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_label_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ] ; + sh:order 29 ; + sh:path rdfs:label ] ; sh:targetClass biolink:VariantToGeneAssociation . biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:property [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path rdfs:label ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 26 ; sh:path biolink:subject_label_closure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 31 ; - sh:path biolink:category ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], + sh:order 2 ; + sh:path biolink:stage_qualifier ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path rdf:predicate ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:iri ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:description ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -19736,16 +19766,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:object ], - [ sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:description ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 32 ; - sh:path rdf:type ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:id ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; @@ -19753,352 +19778,276 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 4 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:qualifiers ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 32 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 31 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], + sh:order 33 ; + sh:path rdfs:label ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 29 ; - sh:path biolink:id ] ; + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:VariantToGeneExpressionAssociation . biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 17 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_object ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:order 28 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category_closure ], + sh:order 20 ; + sh:path biolink:object_category_closure ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 18 ; - sh:path biolink:object_closure ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ], - [ sh:description "total number of things in a particular reference set" ; + sh:order 21 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], - [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:subject_category ], + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], + sh:order 36 ; + sh:path biolink:has_percentage ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:original_predicate ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:original_subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_closure ], [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 22 ; sh:path biolink:object_namespace ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:description ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:order 28 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:iri ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:Onset ; sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 38 ; - sh:path biolink:onset_qualifier ] ; - sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . - -biolink:VariantToPopulationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:path biolink:onset_qualifier ], + [ sh:class biolink:SeverityValue ; + sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_quotient ], - [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_qualifier ], + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 31 ; + sh:order 27 ; sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:description ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 11 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_label_closure ], [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; + sh:order 18 ; sh:path biolink:object_closure ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:id ] ; + sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . + +biolink:VariantToPopulationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path rdf:object ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:description ], - [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20106,113 +20055,159 @@ This field is multi-valued. It should include values for ancestors of the biolin In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:order 32 ; sh:path biolink:category ], - [ sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:description "number all populations that carry a particular allele, aka allele number" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:frequency_qualifier ], + sh:order 1 ; + sh:path biolink:has_total ], + [ sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:publications ], + [ sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_count ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 5 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:description "number all populations that carry a particular allele, aka allele number" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_total ], + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 27 ; sh:path biolink:subject_label_closure ], - [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 2 ; + sh:path biolink:has_quotient ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 30 ; sh:path biolink:id ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_percentage ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:description ], [ sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:order 25 ; sh:path biolink:subject_namespace ], - [ sh:description "number in object population that carry a particular allele, aka allele count" ; + [ sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_count ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 3 ; + sh:path biolink:has_percentage ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path rdf:predicate ], - [ sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 34 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:VariantToPopulationAssociation . biolink:Vertebrate a sh:NodeShape ; sh:closed true ; sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -20221,49 +20216,54 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:order 6 ; - sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ] ; + sh:path biolink:id ] ; sh:targetClass biolink:Vertebrate . biolink:Virus a sh:NodeShape ; sh:closed true ; sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], @@ -20271,11 +20271,12 @@ biolink:Virus a sh:NodeShape ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -20290,46 +20291,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Virus . biolink:WebPage a sh:NodeShape ; sh:closed true ; sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "keywords tagging a publication" ; + sh:property [ sh:description "keywords tagging a publication" ; sh:order 3 ; sh:path biolink:keywords ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:rights ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], @@ -20339,23 +20325,24 @@ biolink:WebPage a sh:NodeShape ; [ sh:maxCount 1 ; sh:order 16 ; sh:path biolink:description ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:order 14 ; sh:path rdf:type ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20369,22 +20356,48 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 9 ; sh:path biolink:creation_date ], + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ] ; sh:targetClass biolink:WebPage . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20394,70 +20407,55 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Behavior . biolink:BehavioralFeature a sh:NodeShape ; sh:closed true ; sh:description "A phenotypic feature which is behavioral in nature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -20466,107 +20464,121 @@ biolink:BehavioralFeature a sh:NodeShape ; [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], - [ sh:order 6 ; - sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ] ; sh:targetClass biolink:BehavioralFeature . biolink:BiologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; sh:path biolink:xref ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ] ; sh:targetClass biolink:BiologicalProcess . biolink:Case a sh:NodeShape ; sh:closed true ; sh:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20576,39 +20588,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ] ; sh:targetClass biolink:Case . biolink:CellLine a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], @@ -20617,46 +20616,63 @@ biolink:CellLine a sh:NodeShape ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 2 ; sh:path biolink:xref ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:CellLine . biolink:CellularComponent a sh:NodeShape ; sh:closed true ; sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:order 6 ; sh:path rdf:type ], [ sh:class biolink:Attribute ; @@ -20673,51 +20689,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:CellularComponent . biolink:ClinicalAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20727,51 +20729,44 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ] ; sh:targetClass biolink:ClinicalAttribute . biolink:Dataset a sh:NodeShape ; sh:closed true ; sh:description "an item that refers to a collection of data from a data source." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:property [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20781,37 +20776,42 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ] ; @@ -20821,48 +20821,51 @@ biolink:DatasetDistribution a sh:NodeShape ; sh:closed true ; sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:creation_date ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:property [ sh:order 10 ; + sh:path rdf:type ], [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:format ], + sh:order 2 ; + sh:path biolink:rights ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:rights ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:description ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:creation_date ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:distribution_download_url ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20871,21 +20874,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 9 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:license ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:DatasetDistribution . biolink:Device a sh:NodeShape ; sh:closed true ; sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], + [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20895,37 +20901,57 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Device . biolink:Exon a sh:NodeShape ; sh:closed true ; sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -20934,11 +20960,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 12 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:order 13 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -20949,101 +20982,42 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 9 ; sh:path biolink:provided_by ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:is_metabolite ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:order 13 ; - sh:path rdf:type ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ] ; + sh:path biolink:is_metabolite ] ; sh:targetClass biolink:Exon . biolink:GeneFamily a sh:NodeShape ; sh:closed true ; sh:description "any grouping of multiple genes or gene products related by common descent" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], + [ sh:order 7 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21052,20 +21026,46 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 6 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GeneFamily . biolink:GeneProductMixin a sh:NodeShape ; sh:closed false ; sh:description "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 2 ; sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ] ; @@ -21075,17 +21075,40 @@ biolink:GeneticInheritance a sh:NodeShape ; sh:closed true ; sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:order 6 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21094,45 +21117,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 5 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:targetClass biolink:GeneticInheritance . + +biolink:InformationContentEntity a sh:NodeShape ; + sh:closed false ; + sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; + sh:order 5 ; sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; - sh:path rdfs:label ], + sh:path biolink:iri ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ] ; - sh:targetClass biolink:GeneticInheritance . - -biolink:InformationContentEntity a sh:NodeShape ; - sh:closed false ; - sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21145,57 +21160,34 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:order 9 ; - sh:path rdf:type ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:InformationContentEntity . biolink:InformationResource a sh:NodeShape ; sh:closed true ; sh:description "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 4 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], [ sh:description "the status of the infores identifier, the default is \"released\"" ; sh:in ( "released" "deprecated" "draft" "modified" ) ; sh:maxCount 1 ; @@ -21203,44 +21195,49 @@ biolink:InformationResource a sh:NodeShape ; sh:path biolink:status ], [ sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:description ] ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 4 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:InformationResource . biolink:OrganismalEntity a sh:NodeShape ; sh:closed false ; sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21250,9 +21247,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ] ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:order 6 ; + sh:path rdf:type ] ; sh:targetClass biolink:OrganismalEntity . biolink:Outcome a sh:NodeShape ; @@ -21265,113 +21265,114 @@ biolink:PredicateMapping a sh:NodeShape ; sh:closed true ; sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], - [ sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:order 17 ; + sh:path biolink:species_context_qualifier ], + [ sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 12 ; + sh:path biolink:object_part_qualifier ], [ sh:class biolink:NamedThing ; sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:exact_match ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_aspect_qualifier ], [ sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_qualifier ], + [ sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:object_context_qualifier ], [ sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:qualified_predicate ], [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:object_part_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_part_qualifier ], [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], - [ sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:object_context_qualifier ], + sh:order 20 ; + sh:path biolink:broad_match ], [ sh:maxCount 1 ; sh:order 5 ; sh:path biolink:subject_derivative_qualifier ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 7 ; sh:path rdf:predicate ], [ sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 0 ; + sh:path biolink:mapped_predicate ], [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:object_direction_qualifier ], - [ sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:narrow_match ], [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_part_qualifier ] ; + sh:order 11 ; + sh:path biolink:object_form_or_variant_qualifier ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; sh:closed true ; sh:description "A series of actions conducted in a certain order or manner" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_attribute ], + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:iri ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:description ], @@ -21384,30 +21385,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Procedure . - -biolink:SocioeconomicAttribute a sh:NodeShape ; - sh:closed true ; - sh:description "Attributes relating to a socioeconomic manifestation" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:Procedure . + +biolink:SocioeconomicAttribute a sh:NodeShape ; + sh:closed true ; + sh:description "Attributes relating to a socioeconomic manifestation" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; @@ -21421,19 +21410,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -21441,6 +21417,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; @@ -21451,47 +21440,103 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 10 ; - sh:path biolink:description ] ; + sh:path biolink:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:Treatment a sh:NodeShape ; sh:closed true ; sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:timepoint ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a point in time" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:timepoint ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:class biolink:Device ; + sh:description "connects an entity to one or more (medical) devices" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_device ], [ sh:class biolink:Drug ; sh:description "connects an entity to one or more drugs" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_drug ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:Treatment . + +biolink:Zygosity a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21501,30 +21546,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Device ; - sh:description "connects an entity to one or more (medical) devices" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_device ] ; - sh:targetClass biolink:Treatment . - -biolink:Zygosity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -21534,133 +21569,98 @@ biolink:Zygosity a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; sh:path rdfs:label ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:Zygosity . biolink:Drug a sh:NodeShape ; sh:closed true ; sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:ChemicalMixture ; - sh:description "" ; + sh:property [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:is_supplement ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:description "" ; + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 3 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:trade_name ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 4 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path biolink:xref ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_chemical_role ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 10 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ] ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalMixture ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:is_supplement ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:order 14 ; + sh:path rdf:type ] ; sh:targetClass biolink:Drug . biolink:ExposureEvent a sh:NodeShape ; @@ -21682,13 +21682,17 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:closed true ; sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21698,68 +21702,57 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:order 6 ; - sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ] ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:IndividualOrganism . biolink:MaterialSample a sh:NodeShape ; sh:closed true ; sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:order 5 ; - sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:order 5 ; + sh:path rdf:type ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21768,21 +21761,21 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 4 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ] ; sh:targetClass biolink:MaterialSample . biolink:Transcript a sh:NodeShape ; sh:closed true ; sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -21791,127 +21784,134 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 12 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_metabolite ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:iri ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:order 13 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; + [ sh:order 13 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:description ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_metabolite ] ; + sh:order 1 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Transcript . biolink:Pathway a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:has_input ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 5 ; sh:path biolink:provided_by ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ] ; + sh:path biolink:id ] ; sh:targetClass biolink:Pathway . biolink:LifeStage a sh:NodeShape ; @@ -21929,9 +21929,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:order 6 ; sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -21941,60 +21941,74 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:LifeStage . biolink:NucleicAcidEntity a sh:NodeShape ; sh:closed true ; sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:order 13 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:class biolink:ChemicalEntity ; + sh:property [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:order 13 ; + sh:path rdf:type ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 3 ; + sh:path biolink:is_metabolite ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 14 ; @@ -22003,24 +22017,21 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_metabolite ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:description ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22029,55 +22040,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 12 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:description ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:closed true ; sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22087,9 +22074,22 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ] ; + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; @@ -22102,74 +22102,124 @@ biolink:MolecularActivity a sh:NodeShape ; sh:closed true ; sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "The gene product, gene, or complex that catalyzes the reaction" ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the input for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the output for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:MolecularActivity . + +biolink:ChemicalMixture a sh:NodeShape ; + sh:closed true ; + sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; sh:minCount 1 ; - sh:order 8 ; + sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; + sh:order 11 ; sh:path biolink:id ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; + sh:order 10 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "The gene product, gene, or complex that catalyzes the reaction" ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:order 9 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:order 14 ; sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the output for the reaction" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the input for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ] ; - sh:targetClass biolink:MolecularActivity . - -biolink:ChemicalMixture a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:is_toxic ], + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; @@ -22181,70 +22231,20 @@ biolink:ChemicalMixture a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ] ; + sh:path biolink:trade_name ] ; sh:targetClass biolink:ChemicalMixture . biolink:MacromolecularMachineMixin a sh:NodeShape ; @@ -22261,13 +22261,10 @@ biolink:MolecularEntity a sh:NodeShape ; sh:closed true ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:property [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22282,46 +22279,49 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 8 ; sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:description ], [ sh:description "" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:trade_name ], - [ sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:description ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:order 11 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 2 ; @@ -22332,26 +22332,16 @@ biolink:PhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -22370,6 +22360,16 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -22381,10 +22381,16 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:closed true ; sh:description "An entity that has material reality (a.k.a. physical essence)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:order 5 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22394,26 +22400,20 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -22423,47 +22423,25 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:Genotype a sh:NodeShape ; sh:closed true ; - sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_biological_sequence ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:class biolink:Zygosity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:order 8 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], + [ sh:class biolink:Zygosity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 6 ; @@ -22476,112 +22454,134 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 7 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:order 8 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Genotype . biolink:SequenceVariant a sh:NodeShape ; sh:closed true ; sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 2 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], [ sh:class biolink:Gene ; sh:description "Each allele can be associated with any number of genes" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:order 8 ; sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ] ; sh:targetClass biolink:SequenceVariant . biolink:Agent a sh:NodeShape ; sh:closed true ; sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; sh:maxCount 1 ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:description ], + [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:order 0 ; + sh:path biolink:affiliation ], + [ sh:order 7 ; + sh:path rdf:type ], [ sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:address ], + [ sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 4 ; sh:path biolink:id ], - [ sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; - sh:order 0 ; - sh:path biolink:affiliation ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 5 ; @@ -22592,26 +22592,7 @@ biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 6 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -22620,18 +22601,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:order 6 ; + sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ] ; @@ -22641,18 +22641,32 @@ biolink:Disease a sh:NodeShape ; sh:closed true ; sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 7 ; sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22662,28 +22676,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Disease . biolink:BiologicalSex a sh:NodeShape ; @@ -22694,30 +22694,6 @@ biolink:BiologicalSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -22730,13 +22706,37 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:BlankNode ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:iri ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; sh:path biolink:xref ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], @@ -22751,14 +22751,17 @@ biolink:Gene a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:property [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:description ], [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_biological_sequence ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], @@ -22771,23 +22774,6 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_biological_sequence ], - [ sh:order 9 ; - sh:path rdf:type ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -22797,9 +22783,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 0 ; sh:path biolink:symbol ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:in_taxon ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 1 ; sh:path biolink:synonym ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -22811,13 +22811,17 @@ biolink:AnatomicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A subcellular location, cell type or gross anatomical part" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22827,54 +22831,69 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:AnatomicalEntity . biolink:ChemicalRole a sh:NodeShape ; sh:closed true ; sh:description " A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 5 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22884,38 +22903,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:path biolink:xref ] ; sh:targetClass biolink:ChemicalRole . biolink:GeneOrGeneProduct a sh:NodeShape ; @@ -22932,19 +22932,7 @@ biolink:Onset a sh:NodeShape ; sh:closed true ; sh:description "The age group in which (disease) symptom manifestations appear" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -22953,63 +22941,60 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:Onset . biolink:SeverityValue a sh:NodeShape ; sh:closed true ; sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -23018,10 +23003,13 @@ biolink:SeverityValue a sh:NodeShape ; [ sh:maxCount 1 ; sh:order 10 ; sh:path biolink:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23031,6 +23019,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -23038,13 +23038,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -23070,94 +23070,76 @@ biolink:ChemicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 12 ; sh:path biolink:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:trade_name ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:max_tolerated_dose ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:order 10 ; sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 6 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_toxic ] ; sh:targetClass biolink:ChemicalEntity . biolink:NamedThing a sh:NodeShape ; sh:closed true ; sh:description "a databased entity or concept/class" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; + sh:property [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:description ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:iri ], - [ sh:order 5 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23172,33 +23154,34 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:NamedThing . - -biolink:OrganismTaxon a sh:NodeShape ; - sh:closed true ; - sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path rdfs:label ], [ sh:order 5 ; sh:path rdf:type ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ] ; + sh:targetClass biolink:NamedThing . + +biolink:OrganismTaxon a sh:NodeShape ; + sh:closed true ; + sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 8 ; @@ -23206,6 +23189,17 @@ biolink:OrganismTaxon a sh:NodeShape ; [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:description ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23215,32 +23209,23 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 4 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:iri ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 6 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:order 5 ; + sh:path rdf:type ] ; sh:targetClass biolink:OrganismTaxon . biolink:EvidenceType a sh:NodeShape ; sh:closed true ; sh:description "Class of evidence that supports an association" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -23249,19 +23234,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 11 ; + sh:path biolink:description ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; @@ -23270,24 +23262,70 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 3 ; sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 5 ; sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ] ; + [ sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:EvidenceType . biolink:Publication a sh:NodeShape ; sh:closed true ; sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). " ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "mesh terms tagging a publication" ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "mesh terms tagging a publication" ; sh:order 4 ; sh:path biolink:mesh_terms ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:format ], + [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:creation_date ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:description "keywords tagging a publication" ; sh:order 3 ; sh:path biolink:keywords ], + [ sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:description ], + [ sh:order 14 ; + sh:path rdf:type ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23297,177 +23335,107 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 13 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], - [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:order 14 ; - sh:path rdf:type ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:description ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], + sh:order 12 ; + sh:path biolink:iri ], [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ] ; + [ sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ] ; sh:targetClass biolink:Publication . biolink:RetrievalSource a sh:NodeShape ; sh:closed true ; sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:format ], - [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:resource_id ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 8 ; sh:path biolink:provided_by ], + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ], [ sh:maxCount 1 ; sh:order 5 ; sh:path biolink:rights ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:upstream_resource_ids ], [ sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:description ], + sh:order 6 ; + sh:path biolink:format ], [ sh:order 12 ; sh:path rdf:type ], + [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:resource_id ], [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:resource_role ], - [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:upstream_resource_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:description ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:RetrievalSource . biolink:Attribute a sh:NodeShape ; sh:closed true ; sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23477,14 +23445,46 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 8 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ] ; + [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; diff --git a/biolink-model.ttl b/biolink-model.ttl index 9ec3feb5d7..1ff2ed8cfb 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -1,11 +1,14 @@ @prefix OIO: . +@prefix dcat: . @prefix dcterms: . +@prefix foaf: . @prefix linkml: . @prefix owl: . @prefix pav: . +@prefix prov: . @prefix rdf: . @prefix rdfs: . -@prefix schema: . +@prefix schema1: . @prefix shex: . @prefix skos: . @prefix xsd: . @@ -346,269 +349,269 @@ , , ; - linkml:generation_date "2023-05-23T23:05:03"^^xsd:dateTime ; + linkml:generation_date "2023-05-23T23:23:18"^^xsd:dateTime ; linkml:id ; linkml:imports , linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SPDI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], - [ linkml:prefix_prefix "MI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBbt" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gtpo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foaf" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COG" ; + linkml:prefixes [ linkml:prefix_prefix "COG" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.compound" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MmusDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "METANETX.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "PomBase" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBls" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ncats.drug" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CLINVAR" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PANTHER.FAMILY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "metacyc.reaction" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Xenbase" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "wgs" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "bioschemas" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCIT-OBO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HsapDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.PATHWAYS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.PATHWAY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.DISEASE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COAR_RESOURCE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMEDCT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NBO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "NCBIGene" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "VMC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "medgen" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "AspGD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], + [ linkml:prefix_prefix "PHARMGKB.CHEMICAL" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "MAXO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.compound" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference dcat: ], + [ linkml:prefix_prefix "CTD.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference foaf: ], + [ linkml:prefix_prefix "gtpo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcid" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HCPCS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ChemBank" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "AspGD" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MmusDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ScopusID" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "EDAM-TOPIC" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "STY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EFO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ORCID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UMLSSG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG" ; 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+ linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COAR_RESOURCE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXCUI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MESH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DOID-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SPDI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "medgen" ; + linkml:prefix_reference ] ; linkml:slots , , , @@ -1311,7 +1314,7 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2023-05-23T23:03:00"^^xsd:dateTime ; + linkml:source_file_date "2023-05-23T23:21:51"^^xsd:dateTime ; linkml:source_file_size 356228 ; linkml:subsets , , @@ -1417,7 +1420,7 @@ a linkml:TypeDefinition ; skos:definition "The combination of a date and time" ; - skos:exactMatch schema:DateTime ; + skos:exactMatch schema1:DateTime ; skos:inScheme linkml:types ; linkml:base "XSDDateTime" ; linkml:definition_uri linkml:Datetime ; @@ -1426,7 +1429,7 @@ linkml:uri xsd:dateTime . a linkml:TypeDefinition ; - skos:broadMatch schema:Number ; + skos:broadMatch schema1:Number ; skos:definition "A real number with arbitrary precision that conforms to the xsd:decimal specification" ; skos:inScheme linkml:types ; linkml:base "Decimal" ; @@ -1660,7 +1663,7 @@ linkml:is_a . a linkml:TypeDefinition ; - skos:closeMatch schema:URL ; + skos:closeMatch schema1:URL ; skos:definition "a complete URI" ; skos:inScheme linkml:types ; skos:note "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" ; @@ -2088,9 +2091,9 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:example "cerebral cortext" ], + skos:example "blood" ], [ a linkml:Example ; - skos:example "blood" ] ; + skos:example "cerebral cortext" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -2256,9 +2259,9 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:example "human" ], + skos:example "zebrafish" ], [ a linkml:Example ; - skos:example "zebrafish" ] ; + skos:example "human" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -3172,11 +3175,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "abnormal brain ventricle size" ; - skos:example "MP:0013229" ], - [ a linkml:Example ; skos:definition "Ehlers-Danlos syndrome, vascular type" ; - skos:example "MONDO:0017314" ] ; + skos:example "MONDO:0017314" ], + [ a linkml:Example ; + skos:definition "abnormal brain ventricle size" ; + skos:example "MP:0013229" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "annotation subject" ; @@ -3554,14 +3557,14 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; + skos:definition "axon morphology variant" ; + skos:example "WBPhenotype:0000180" ], + [ a linkml:Example ; skos:definition "abnormal circulating bilirubin level" ; skos:example "MP:0001569" ], [ a linkml:Example ; skos:definition "Hyperkinesis" ; - skos:example "HP:0002487" ], - [ a linkml:Example ; - skos:definition "axon morphology variant" ; - skos:example "WBPhenotype:0000180" ] ; + skos:example "HP:0002487" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -6068,7 +6071,7 @@ a linkml:TypeDefinition ; skos:definition "A time object represents a (local) time of day, independent of any particular day" ; skos:editorialNote "URI is dateTime because OWL reasoners do not work with straight date or time" ; - skos:exactMatch schema:Time ; + skos:exactMatch schema1:Time ; skos:inScheme linkml:types ; linkml:base "XSDTime" ; linkml:definition_uri linkml:Time ; @@ -8425,23 +8428,23 @@ a linkml:SlotDefinition ; skos:inScheme ; - skos:mappingRelation ; + skos:mappingRelation dcat:downloadURL ; linkml:definition_uri ; linkml:domain ; linkml:is_a ; linkml:owner ; linkml:range ; - linkml:slot_uri . + linkml:slot_uri dcat:downloadURL . a linkml:SlotDefinition ; skos:inScheme ; - skos:mappingRelation ; + skos:mappingRelation dcat:downloadURL ; linkml:definition_uri ; linkml:domain ; linkml:is_a ; linkml:owner ; linkml:range ; - linkml:slot_uri . + linkml:slot_uri dcat:downloadURL . a linkml:SlotDefinition ; skos:definition "A list of terms from different schemas or terminology systems that have an identical meaning. Such terms often describe the same concept from different ontological perspectives." ; @@ -8690,14 +8693,14 @@ a linkml:SlotDefinition ; skos:inScheme ; - skos:mappingRelation schema:logo ; + skos:mappingRelation schema1:logo ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; linkml:is_a ; linkml:owner ; linkml:range ; - linkml:slot_uri schema:logo . + linkml:slot_uri schema1:logo . a linkml:SlotDefinition ; OIO:inSubset ; @@ -9936,7 +9939,7 @@ a linkml:TypeDefinition ; skos:definition "a date (year, month and day) in an idealized calendar" ; skos:editorialNote "URI is dateTime because OWL reasoners don't work with straight date or time" ; - skos:exactMatch schema:Date ; + skos:exactMatch schema1:Date ; skos:inScheme linkml:types ; linkml:base "XSDDate" ; linkml:definition_uri linkml:Date ; @@ -9945,7 +9948,7 @@ linkml:uri xsd:date . a linkml:SlotDefinition ; - skos:exactMatch ; + skos:exactMatch dcat:downloadURL ; skos:inScheme ; linkml:definition_uri ; linkml:domain ; @@ -10296,7 +10299,7 @@ skos:altLabel "descriptors", "topic" ; skos:definition "Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred. See https://github.com/biolink/biolink-model/issues/238" ; - skos:exactMatch ; + skos:exactMatch foaf:topic ; skos:inScheme ; linkml:definition_uri ; linkml:domain ; @@ -11889,11 +11892,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "treats" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12090,11 +12093,11 @@ skos:narrowMatch , ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "enables" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12125,11 +12128,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "prevents" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12255,11 +12258,11 @@ skos:inScheme ; skos:mappingRelation ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "is excipient of" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12318,11 +12321,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "has not completed" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has not completed" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12349,11 +12352,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "has increased amount" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12413,11 +12416,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "has decreased amount" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12565,11 +12568,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "has completed" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has completed" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12790,11 +12793,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "decreases response to" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -13075,11 +13078,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "has part" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -13443,11 +13446,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "predisposes" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -13899,11 +13902,11 @@ ; skos:relatedMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "contraindicated for" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -15156,11 +15159,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "exacerbates" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -15179,13 +15182,13 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "abundance" ], + skos:example "stability" ], [ a linkml:Example ; skos:example "exposure" ], [ a linkml:Example ; - skos:example "stability" ], + skos:example "expression" ], [ a linkml:Example ; - skos:example "expression" ] ; + skos:example "abundance" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -15234,7 +15237,7 @@ a linkml:TypeDefinition ; skos:definition "A binary (true or false) value" ; - skos:exactMatch schema:Boolean ; + skos:exactMatch schema1:Boolean ; skos:inScheme linkml:types ; linkml:base "Bool" ; linkml:definition_uri linkml:Boolean ; @@ -15313,9 +15316,9 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "gut microbiome" ], + skos:example "cohort x (e.g. a specific population, referenced by an identifier)" ], [ a linkml:Example ; - skos:example "cohort x (e.g. a specific population, referenced by an identifier)" ] ; + skos:example "gut microbiome" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -15442,15 +15445,15 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "chemical analog" ], + skos:example "late stage" ], [ a linkml:Example ; - skos:example "mutation" ], + skos:example "transplant" ], [ a linkml:Example ; - skos:example "severe" ], + skos:example "chemical analog" ], [ a linkml:Example ; - skos:example "late stage" ], + skos:example "severe" ], [ a linkml:Example ; - skos:example "transplant" ] ; + skos:example "mutation" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -15467,11 +15470,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "postsynaptic membrane" ; - skos:example "GO:0045211" ], - [ a linkml:Example ; skos:definition "kinase activity" ; - skos:example "GO:0016301" ] ; + skos:example "GO:0016301" ], + [ a linkml:Example ; + skos:definition "postsynaptic membrane" ; + skos:example "GO:0045211" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:local_names [ linkml:ga4gh [ skos:altLabel "descriptor" ; @@ -16567,7 +16570,7 @@ linkml:slot_uri . a linkml:TypeDefinition ; - skos:closeMatch schema:Float ; + skos:closeMatch schema1:Float ; skos:definition "A real number that conforms to the xsd:double specification" ; skos:inScheme linkml:types ; linkml:base "float" ; @@ -16626,11 +16629,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -16877,7 +16880,7 @@ skos:definition "an item that refers to a collection of data from a data source." ; skos:exactMatch , , - schema:dataset, + schema1:dataset, ; skos:inScheme ; linkml:class_uri ; @@ -20165,7 +20168,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t a linkml:TypeDefinition ; skos:definition "A real number that conforms to the xsd:float specification" ; - skos:exactMatch schema:Float ; + skos:exactMatch schema1:Float ; skos:inScheme linkml:types ; linkml:base "float" ; linkml:definition_uri linkml:Float ; @@ -20862,11 +20865,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t , ; linkml:annotations [ a linkml:Annotation ; - skos:example "has output" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has output" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:domain_of ; @@ -22004,7 +22007,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t a linkml:TypeDefinition ; skos:definition "An integer" ; - skos:exactMatch schema:Integer ; + skos:exactMatch schema1:Integer ; skos:inScheme linkml:types ; linkml:base "int" ; linkml:definition_uri linkml:Integer ; @@ -22717,11 +22720,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:inScheme ; skos:note "This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)" ; linkml:alt_descriptions [ a linkml:AltDescription ; - skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; - linkml:source "AGR" ], - [ a linkml:AltDescription ; skos:definition "A contiguous change at a Location" ; - linkml:source "VMC" ] ; + linkml:source "VMC" ], + [ a linkml:AltDescription ; + skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; + linkml:source "AGR" ] ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "AGRKB", @@ -22832,7 +22835,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t a linkml:ClassDefinition ; rdfs:seeAlso ; skos:definition "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; - skos:exactMatch schema:Class, + skos:exactMatch schema1:Class, owl:Class ; skos:inScheme ; skos:note "Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity", @@ -23376,7 +23379,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t a linkml:TypeDefinition ; skos:definition "A character string" ; - skos:exactMatch schema:Text ; + skos:exactMatch schema1:Text ; skos:inScheme linkml:types ; linkml:base "str" ; linkml:definition_uri linkml:String ; diff --git a/biolink/model.py b/biolink/model.py index 34482ca22f..79806af7dc 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-05-23T23:05:19 +# Generation date: 2023-05-23T23:23:30 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model diff --git a/biolink/pydanticmodel.py b/biolink/pydanticmodel.py new file mode 100644 index 0000000000..9069614de5 --- /dev/null +++ b/biolink/pydanticmodel.py @@ -0,0 +1,8655 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +from linkml_runtime.linkml_model import Decimal +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +metamodel_version = "None" +version = "3.4.0" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class DirectionQualifierEnum(str, Enum): + + + increased = "increased" + + upregulated = "upregulated" + + decreased = "decreased" + + downregulated = "downregulated" + + + +class ChemicalEntityDerivativeEnum(str, Enum): + + + metabolite = "metabolite" + + + +class ChemicalOrGeneOrGeneProductFormOrVariantEnum(str, Enum): + + + genetic_variant_form = "genetic_variant_form" + + modified_form = "modified_form" + + loss_of_function_variant_form = "loss_of_function_variant_form" + + gain_of_function_variant_form = "gain_of_function_variant_form" + + polymorphic_form = "polymorphic_form" + + snp_form = "snp_form" + + analog_form = "analog_form" + + + +class GeneOrGeneProductOrChemicalPartQualifierEnum(str, Enum): + + + number_3_prime_utr = "3_prime_utr" + + number_5_prime_utr = "5_prime_utr" + + polya_tail = "polya_tail" + + promoter = "promoter" + + enhancer = "enhancer" + + exon = "exon" + + intron = "intron" + + + +class GeneOrGeneProductOrChemicalEntityAspectEnum(str, Enum): + + # Used in cases where the specificity of the relationship can not be determined to be either activity or abundance. In general, a more specific value from this enumeration should be used. + activity_or_abundance = "activity_or_abundance" + + abundance = "abundance" + + activity = "activity" + + expression = "expression" + + synthesis = "synthesis" + + degradation = "degradation" + + cleavage = "cleavage" + + hydrolysis = "hydrolysis" + + metabolic_processing = "metabolic_processing" + + mutation_rate = "mutation_rate" + + stability = "stability" + + folding = "folding" + + localization = "localization" + + transport = "transport" + + secretion = "secretion" + + uptake = "uptake" + + molecular_modification = "molecular_modification" + + acetylation = "acetylation" + + acylation = "acylation" + + alkylation = "alkylation" + + amination = "amination" + + carbamoylation = "carbamoylation" + + ethylation = "ethylation" + + glutathionylation = "glutathionylation" + + glycation = "glycation" + + glycosylation = "glycosylation" + + glucuronidation = "glucuronidation" + + n_linked_glycosylation = "n_linked_glycosylation" + + o_linked_glycosylation = "o_linked_glycosylation" + + hydroxylation = "hydroxylation" + + lipidation = "lipidation" + + farnesylation = "farnesylation" + + geranoylation = "geranoylation" + + myristoylation = "myristoylation" + + palmitoylation = "palmitoylation" + + prenylation = "prenylation" + + methylation = "methylation" + + nitrosation = "nitrosation" + + nucleotidylation = "nucleotidylation" + + phosphorylation = "phosphorylation" + + ribosylation = "ribosylation" + + ADP_ribosylation = "ADP-ribosylation" + + sulfation = "sulfation" + + sumoylation = "sumoylation" + + ubiquitination = "ubiquitination" + + oxidation = "oxidation" + + reduction = "reduction" + + carboxylation = "carboxylation" + + + +class CausalMechanismQualifierEnum(str, Enum): + + # A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction. + binding = "binding" + # A causal mechanism in which the effector binds to the target and negatively effects its normal function, e.g. prevention of enzymatic reaction or activation of downstream pathway. + inhibition = "inhibition" + # A causal mechanism in which an antibody specifically binds to and interferes with the target. + antibody_inhibition = "antibody_inhibition" + # A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist through competing for the binding site. + antagonism = "antagonism" + # A causal mechanism in which the effector binds to a molecular channel and prevents or reduces transport of ions through it. + molecular_channel_blockage = "molecular_channel_blockage" + # A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling. + inverse_agonism = "inverse_agonism" + # A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition) + negative_allosteric_modulation = "negative_allosteric_modulation" + # A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an endogenous ligand. + agonism = "agonism" + # A causal mechanism in which the effector binds to a molecular channel and facilitates transport of ions through it. + molecular_channel_opening = "molecular_channel_opening" + # A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition) + positive_allosteric_modulation = "positive_allosteric_modulation" + # A causal mechanism in which the effector binds to and enhances or intensifies the effect of some other chemical or drug on its target. + potentiation = "potentiation" + # A causal mechanism in which the effector binds to and positively affects the normal functioning of its target. + activation = "activation" + # A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that processes drugs in the body. + inducer = "inducer" + # A causal mechanism mediated by through the control of target gene transcription + transcriptional_regulation = "transcriptional_regulation" + # A causal mechanism mediated by the activation or control of signaling events that influence the some aspect of the target entity (e.g. its activity, processing, transport, etc) + signaling_mediated_control = "signaling_mediated_control" + + stabilization = "stabilization" + + stimulation = "stimulation" + + releasing_activity = "releasing_activity" + + + +class LogicalInterpretationEnum(str, Enum): + + # A modifier on a triple that causes the triple to be interpreted as a some-some statement + some_some = "some_some" + # A modifier on a triple that causes the triple to be interpreted as an all-some statement. + all_some = "all_some" + + inverse_all_some = "inverse_all_some" + + + +class ReactionDirectionEnum(str, Enum): + + + left_to_right = "left_to_right" + + right_to_left = "right_to_left" + + bidirectional = "bidirectional" + + neutral = "neutral" + + + +class ReactionSideEnum(str, Enum): + + + left = "left" + + right = "right" + + + +class PhaseEnum(str, Enum): + """ + phase + """ + + number_0 = "0" + + number_1 = "1" + + number_2 = "2" + + + +class StrandEnum(str, Enum): + """ + strand + """ + # Positive + PLUS_SIGN = "+" + # Negative + _ = "-" + # Unstranded + FULL_STOP = "." + # Unknown + QUESTION_MARK = "?" + + + +class SequenceEnum(str, Enum): + """ + type of sequence + """ + # nucleic acid + na = "na" + # amino acid + aa = "aa" + + + +class DruggableGeneCategoryEnum(str, Enum): + + # These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action. + tclin = "tclin" + # These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy the activity thresholds detailed below. + tbio = "tbio" + # These targets do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy one or more of the following criteria: target is above the cutoff criteria for Tdark target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s) with an Experimental Evidence code + tchem = "tchem" + # These are targets about which virtually nothing is known. They do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy two or more of the following criteria: A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or less than or equal to 50 Antibodies available according to http://antibodypedia.com. + tdark = "tdark" + + + +class DrugAvailabilityEnum(str, Enum): + + # chemical entity is available over the counter without a prescription. + over_the_counter = "over_the_counter" + # chemical entity is available by prescription. + prescription = "prescription" + + + +class DrugDeliveryEnum(str, Enum): + + + inhalation = "inhalation" + + oral = "oral" + + absorption_through_the_skin = "absorption_through_the_skin" + + intravenous_injection = "intravenous_injection" + + + +class ResourceRoleEnum(str, Enum): + """ + The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience. + """ + + primary_knowledge_source = "primary_knowledge_source" + + aggregator_knowledge_source = "aggregator_knowledge_source" + + supporting_data_source = "supporting_data_source" + + + +class FDAApprovalStatusEnum(str, Enum): + + # Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments. + discovery_and_development_phase = "discovery_and_development_phase" + # Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo. + preclinical_research_phase = "preclinical_research_phase" + # Clinical Research Phase. Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer. + fda_clinical_research_phase = "fda_clinical_research_phase" + # FDA Review + fda_review_phase_4 = "fda_review_phase_4" + # FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations. + fda_post_market_safety_review = "fda_post_market_safety_review" + # In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase. + fda_clinical_research_phase_1 = "fda_clinical_research_phase_1" + # In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur. + fda_clinical_research_phase_2 = "fda_clinical_research_phase_2" + # In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions. + fda_clinical_research_phase_3 = "fda_clinical_research_phase_3" + # In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review. + fda_clinical_research_phase_4 = "fda_clinical_research_phase_4" + # Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track + fda_fast_track = "fda_fast_track" + # Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy + fda_breakthrough_therapy = "fda_breakthrough_therapy" + # When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval + fda_accelerated_approval = "fda_accelerated_approval" + # Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times – Standard Review and Priority Review. A Priority Review designation means FDA’s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review + fda_priority_review = "fda_priority_review" + # Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations. + regular_fda_approval = "regular_fda_approval" + + post_approval_withdrawal = "post_approval_withdrawal" + + + +class FDAIDAAdverseEventEnum(str, Enum): + """ + please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32 + """ + # An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. It does not include an adverse event or suspected adverse reaction that, had it occurred in a more severe form, might have caused death. + life_threatening_adverse_event = "life_threatening_adverse_event" + # An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event, inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth defect. Important medical events that may not result in death, be life-threatening, or require hospitalization may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or subject and may require medical or surgical intervention to prevent one of the outcomes listed in this definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient hospitalization, or the development of drug dependency or drug abuse. + serious_adverse_event = "serious_adverse_event" + # means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug. + suspected_adverse_reaction = "suspected_adverse_reaction" + # An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the investigator brochure or is not listed at the specificity or severity that has been observed; or, if an investigator brochure is not required or available, is not consistent with the risk information described in the general investigational plan or elsewhere in the current application, as amended. For example, under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but are not specifically mentioned as occurring with the particular drug under investigation. + unexpected_adverse_event = "unexpected_adverse_event" + + + +class InformationResourceStatusEnum(str, Enum): + + + released = "released" + + deprecated = "deprecated" + + draft = "draft" + + modified = "modified" + + + +class MappingCollection(ConfiguredBaseModel): + """ + A collection of deprecated mappings. + """ + predicate_mappings: Optional[List[PredicateMapping]] = Field(None, description="""A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3.""") + + + +class PredicateMapping(ConfiguredBaseModel): + """ + A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place. + """ + mapped_predicate: Optional[str] = Field(None, description="""The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.""") + subject_aspect_qualifier: Optional[str] = Field(None) + subject_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + subject_form_or_variant_qualifier: Optional[str] = Field(None) + subject_part_qualifier: Optional[str] = Field(None) + subject_derivative_qualifier: Optional[str] = Field(None) + subject_context_qualifier: Optional[str] = Field(None) + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + qualified_predicate: Optional[str] = Field(None, description="""Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.""") + object_aspect_qualifier: Optional[str] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + object_form_or_variant_qualifier: Optional[str] = Field(None) + object_part_qualifier: Optional[str] = Field(None) + object_derivative_qualifier: Optional[str] = Field(None) + object_context_qualifier: Optional[str] = Field(None) + causal_mechanism_qualifier: Optional[CausalMechanismQualifierEnum] = Field(None, description="""A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") + species_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.""") + exact_match: Optional[List[str]] = Field(None, description="""holds between two entities that have strictly equivalent meanings, with a high degree of confidence""") + narrow_match: Optional[List[str]] = Field(None, description="""a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.""") + broad_match: Optional[List[str]] = Field(None, description="""a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.""") + + + +class OntologyClass(ConfiguredBaseModel): + """ + a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type. + """ + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + + + +class Annotation(ConfiguredBaseModel): + """ + Biolink Model root class for entity annotations. + """ + None + + + +class QuantityValue(Annotation): + """ + A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value + """ + has_unit: Optional[str] = Field(None, description="""connects a quantity value to a unit""") + has_numeric_value: Optional[float] = Field(None, description="""connects a quantity value to a number""") + + + +class RelationshipQuantifier(ConfiguredBaseModel): + + None + + + +class SensitivityQuantifier(RelationshipQuantifier): + + None + + + +class SpecificityQuantifier(RelationshipQuantifier): + + None + + + +class PathognomonicityQuantifier(SpecificityQuantifier): + """ + A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease + """ + None + + + +class FrequencyQuantifier(RelationshipQuantifier): + + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + + + +class ChemicalOrDrugOrTreatment(ConfiguredBaseModel): + + None + + + +class Entity(ConfiguredBaseModel): + """ + Root Biolink Model class for all things and informational relationships, real or imagined. + """ + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Entity","biolink:Entity"]] = Field(["biolink:Entity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class NamedThing(Entity): + """ + a databased entity or concept/class + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/NamedThing","biolink:NamedThing"]] = Field(["biolink:NamedThing"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Attribute(NamedThing, OntologyClass): + """ + A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material. + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/Attribute","biolink:Attribute"]] = Field(["biolink:Attribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalRole(Attribute): + """ + A role played by the molecular entity or part thereof within a chemical context. + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalRole","biolink:ChemicalRole"]] = Field(["biolink:ChemicalRole"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class BiologicalSex(Attribute): + + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/BiologicalSex","biolink:BiologicalSex"]] = Field(["biolink:BiologicalSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PhenotypicSex(BiologicalSex): + """ + An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicSex","biolink:PhenotypicSex"]] = Field(["biolink:PhenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GenotypicSex(BiologicalSex): + """ + An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes. + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/GenotypicSex","biolink:GenotypicSex"]] = Field(["biolink:GenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SeverityValue(Attribute): + """ + describes the severity of a phenotypic feature or disease + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/SeverityValue","biolink:SeverityValue"]] = Field(["biolink:SeverityValue"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class RelationshipType(OntologyClass): + """ + An OWL property used as an edge label + """ + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + + + +class TaxonomicRank(OntologyClass): + """ + A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) + """ + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + + + +class OrganismTaxon(NamedThing): + """ + A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies. + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxon","biolink:OrganismTaxon"]] = Field(["biolink:OrganismTaxon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Event(NamedThing): + """ + Something that happens at a given place and time. + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Event","biolink:Event"]] = Field(["biolink:Event"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class AdministrativeEntity(NamedThing): + + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/AdministrativeEntity","biolink:AdministrativeEntity"]] = Field(["biolink:AdministrativeEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Agent(AdministrativeEntity): + """ + person, group, organization or project that provides a piece of information (i.e. a knowledge association) + """ + affiliation: Optional[List[str]] = Field(default_factory=list, description="""a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.""") + address: Optional[str] = Field(None, description="""the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Agent","biolink:Agent"]] = Field(["biolink:Agent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class InformationContentEntity(NamedThing): + """ + a piece of information that typically describes some topic of discourse or is used as support. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/InformationContentEntity","biolink:InformationContentEntity"]] = Field(["biolink:InformationContentEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class StudyResult(InformationContentEntity): + """ + A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/StudyResult","biolink:StudyResult"]] = Field(["biolink:StudyResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class StudyVariable(InformationContentEntity): + """ + a variable that is used as a measure in the investigation of a study + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/StudyVariable","biolink:StudyVariable"]] = Field(["biolink:StudyVariable"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class CommonDataElement(InformationContentEntity): + """ + A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home) + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CommonDataElement","biolink:CommonDataElement"]] = Field(["biolink:CommonDataElement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ConceptCountAnalysisResult(StudyResult): + """ + A result of a concept count analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ConceptCountAnalysisResult","biolink:ConceptCountAnalysisResult"]] = Field(["biolink:ConceptCountAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ObservedExpectedFrequencyAnalysisResult(StudyResult): + """ + A result of a observed expected frequency analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ObservedExpectedFrequencyAnalysisResult","biolink:ObservedExpectedFrequencyAnalysisResult"]] = Field(["biolink:ObservedExpectedFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class RelativeFrequencyAnalysisResult(StudyResult): + """ + A result of a relative frequency analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/RelativeFrequencyAnalysisResult","biolink:RelativeFrequencyAnalysisResult"]] = Field(["biolink:RelativeFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class TextMiningResult(StudyResult): + """ + A result of text mining. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/TextMiningResult","biolink:TextMiningResult"]] = Field(["biolink:TextMiningResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChiSquaredAnalysisResult(StudyResult): + """ + A result of a chi squared analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChiSquaredAnalysisResult","biolink:ChiSquaredAnalysisResult"]] = Field(["biolink:ChiSquaredAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class LogOddsAnalysisResult(StudyResult): + """ + A result of a log odds ratio analysis. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/LogOddsAnalysisResult","biolink:LogOddsAnalysisResult"]] = Field(["biolink:LogOddsAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Dataset(InformationContentEntity): + """ + an item that refers to a collection of data from a data source. + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Dataset","biolink:Dataset"]] = Field(["biolink:Dataset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DatasetDistribution(InformationContentEntity): + """ + an item that holds distribution level information about a dataset. + """ + distribution_download_url: Optional[str] = Field(None) + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DatasetDistribution","biolink:DatasetDistribution"]] = Field(["biolink:DatasetDistribution"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DatasetVersion(InformationContentEntity): + """ + an item that holds version level information about a dataset. + """ + has_dataset: Optional[str] = Field(None) + ingest_date: Optional[str] = Field(None) + has_distribution: Optional[str] = Field(None) + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DatasetVersion","biolink:DatasetVersion"]] = Field(["biolink:DatasetVersion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DatasetSummary(InformationContentEntity): + """ + an item that holds summary level information about a dataset. + """ + source_web_page: Optional[str] = Field(None) + source_logo: Optional[str] = Field(None) + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DatasetSummary","biolink:DatasetSummary"]] = Field(["biolink:DatasetSummary"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ConfidenceLevel(InformationContentEntity): + """ + Level of confidence in a statement + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ConfidenceLevel","biolink:ConfidenceLevel"]] = Field(["biolink:ConfidenceLevel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EvidenceType(InformationContentEntity): + """ + Class of evidence that supports an association + """ + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/EvidenceType","biolink:EvidenceType"]] = Field(["biolink:EvidenceType"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Publication(InformationContentEntity): + """ + Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). + """ + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Publication","biolink:Publication"]] = Field(["biolink:Publication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Book(Publication): + """ + This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. + """ + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Books should have industry-standard identifier such as from ISBN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Book","biolink:Book"]] = Field(["biolink:Book"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'book'.""") + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class BookChapter(Publication): + + published_in: str = Field(..., description="""The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.""") + volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") + chapter: Optional[str] = Field(None, description="""chapter of a book""") + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/BookChapter","biolink:BookChapter"]] = Field(["biolink:BookChapter"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Serial(Publication): + """ + This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. + """ + iso_abbreviation: Optional[str] = Field(None, description="""Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.""") + volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") + issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Serials (journals) should have industry-standard identifier such as from ISSN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Serial","biolink:Serial"]] = Field(["biolink:Serial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'serial' or 'journal'.""") + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Article(Publication): + """ + a piece of writing on a particular topic presented as a stand-alone section of a larger publication + """ + published_in: str = Field(..., description="""The enclosing parent serial containing the article should have industry-standard identifier from ISSN.""") + iso_abbreviation: Optional[str] = Field(None, description="""Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.""") + volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") + issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Article","biolink:Article"]] = Field(["biolink:Article"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class JournalArticle(Article): + """ + an article, typically presenting results of research, that is published in an issue of a scientific journal. + """ + published_in: str = Field(..., description="""The enclosing parent serial containing the article should have industry-standard identifier from ISSN.""") + iso_abbreviation: Optional[str] = Field(None, description="""Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.""") + volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") + issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/JournalArticle","biolink:JournalArticle"]] = Field(["biolink:JournalArticle"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Patent(Publication): + """ + a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. + """ + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Patent","biolink:Patent"]] = Field(["biolink:Patent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class WebPage(Publication): + """ + a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features. + """ + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/WebPage","biolink:WebPage"]] = Field(["biolink:WebPage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PreprintPublication(Publication): + """ + a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal. + """ + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PreprintPublication","biolink:PreprintPublication"]] = Field(["biolink:PreprintPublication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DrugLabel(Publication): + """ + a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. + """ + authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + summary: Optional[str] = Field(None, description="""executive summary of a publication""") + keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DrugLabel","biolink:DrugLabel"]] = Field(["biolink:DrugLabel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class RetrievalSource(InformationContentEntity): + """ + Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved. + """ + resource_id: str = Field(..., description="""The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") + resource_role: ResourceRoleEnum = Field(..., description="""The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge.""") + upstream_resource_ids: Optional[str] = Field(None, description="""The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + license: Optional[str] = Field(None) + rights: Optional[str] = Field(None) + format: Optional[str] = Field(None) + creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/RetrievalSource","biolink:RetrievalSource"]] = Field(["biolink:RetrievalSource"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PhysicalEssenceOrOccurrent(ConfiguredBaseModel): + """ + Either a physical or processual entity. + """ + None + + + +class PhysicalEssence(PhysicalEssenceOrOccurrent): + """ + Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge. + """ + None + + + +class PhysicalEntity(PhysicalEssence, NamedThing): + """ + An entity that has material reality (a.k.a. physical essence). + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PhysicalEntity","biolink:PhysicalEntity"]] = Field(["biolink:PhysicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Occurrent(PhysicalEssenceOrOccurrent): + """ + A processual entity. + """ + None + + + +class ActivityAndBehavior(Occurrent): + """ + Activity or behavior of any independent integral living, organization or mechanical actor in the world + """ + None + + + +class Activity(ActivityAndBehavior, NamedThing): + """ + An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Activity","biolink:Activity"]] = Field(["biolink:Activity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Study(Activity): + """ + a detailed investigation and/or analysis + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Study","biolink:Study"]] = Field(["biolink:Study"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Procedure(ActivityAndBehavior, NamedThing): + """ + A series of actions conducted in a certain order or manner + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Procedure","biolink:Procedure"]] = Field(["biolink:Procedure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Phenomenon(Occurrent, NamedThing): + """ + a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Phenomenon","biolink:Phenomenon"]] = Field(["biolink:Phenomenon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Device(NamedThing): + """ + A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Device","biolink:Device"]] = Field(["biolink:Device"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DiagnosticAid(NamedThing): + """ + A device or substance used to help diagnose disease or injury + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DiagnosticAid","biolink:DiagnosticAid"]] = Field(["biolink:DiagnosticAid"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SubjectOfInvestigation(ConfiguredBaseModel): + """ + An entity that has the role of being studied in an investigation, study, or experiment + """ + None + + + +class MaterialSample(SubjectOfInvestigation, PhysicalEntity): + """ + A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO] + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MaterialSample","biolink:MaterialSample"]] = Field(["biolink:MaterialSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PlanetaryEntity(NamedThing): + """ + Any entity or process that exists at the level of the whole planet + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PlanetaryEntity","biolink:PlanetaryEntity"]] = Field(["biolink:PlanetaryEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EnvironmentalProcess(PlanetaryEntity, Occurrent): + + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalProcess","biolink:EnvironmentalProcess"]] = Field(["biolink:EnvironmentalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EnvironmentalFeature(PlanetaryEntity): + + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFeature","biolink:EnvironmentalFeature"]] = Field(["biolink:EnvironmentalFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeographicLocation(PlanetaryEntity): + """ + a location that can be described in lat/long coordinates + """ + latitude: Optional[float] = Field(None, description="""latitude""") + longitude: Optional[float] = Field(None, description="""longitude""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocation","biolink:GeographicLocation"]] = Field(["biolink:GeographicLocation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeographicLocationAtTime(GeographicLocation): + """ + a location that can be described in lat/long coordinates, for a particular time + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + latitude: Optional[float] = Field(None, description="""latitude""") + longitude: Optional[float] = Field(None, description="""longitude""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocationAtTime","biolink:GeographicLocationAtTime"]] = Field(["biolink:GeographicLocationAtTime"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ThingWithTaxon(ConfiguredBaseModel): + """ + A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + + + +class BiologicalEntity(ThingWithTaxon, NamedThing): + + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/BiologicalEntity","biolink:BiologicalEntity"]] = Field(["biolink:BiologicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GenomicEntity(ConfiguredBaseModel): + + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + + + +class EpigenomicEntity(ConfiguredBaseModel): + + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + + + +class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): + """ + Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system. + """ + has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") + has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") + enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/BiologicalProcessOrActivity","biolink:BiologicalProcessOrActivity"]] = Field(["biolink:BiologicalProcessOrActivity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MolecularActivity(BiologicalProcessOrActivity, Occurrent, OntologyClass): + """ + An execution of a molecular function carried out by a gene product or macromolecular complex. + """ + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + has_input: Optional[List[str]] = Field(None, description="""A chemical entity that is the input for the reaction""") + has_output: Optional[List[str]] = Field(None, description="""A chemical entity that is the output for the reaction""") + enabled_by: Optional[List[str]] = Field(None, description="""The gene product, gene, or complex that catalyzes the reaction""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivity","biolink:MolecularActivity"]] = Field(["biolink:MolecularActivity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class BiologicalProcess(BiologicalProcessOrActivity, Occurrent, OntologyClass): + """ + One or more causally connected executions of molecular functions + """ + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") + has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") + enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/BiologicalProcess","biolink:BiologicalProcess"]] = Field(["biolink:BiologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Pathway(BiologicalProcess, OntologyClass): + + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") + has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") + enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Pathway","biolink:Pathway"]] = Field(["biolink:Pathway"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PhysiologicalProcess(BiologicalProcess, OntologyClass): + + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") + has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") + enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PhysiologicalProcess","biolink:PhysiologicalProcess"]] = Field(["biolink:PhysiologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Behavior(BiologicalProcess, ActivityAndBehavior, OntologyClass): + + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") + has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") + enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Behavior","biolink:Behavior"]] = Field(["biolink:Behavior"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class OrganismAttribute(Attribute): + """ + describes a characteristic of an organismal entity. + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/OrganismAttribute","biolink:OrganismAttribute"]] = Field(["biolink:OrganismAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PhenotypicQuality(OrganismAttribute): + """ + A property of a phenotype + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicQuality","biolink:PhenotypicQuality"]] = Field(["biolink:PhenotypicQuality"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneticInheritance(BiologicalEntity): + """ + The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneticInheritance","biolink:GeneticInheritance"]] = Field(["biolink:GeneticInheritance"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class OrganismalEntity(BiologicalEntity, SubjectOfInvestigation): + """ + A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/OrganismalEntity","biolink:OrganismalEntity"]] = Field(["biolink:OrganismalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Bacterium(OrganismalEntity): + """ + A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Bacterium","biolink:Bacterium"]] = Field(["biolink:Bacterium"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Virus(OrganismalEntity, SubjectOfInvestigation): + """ + A virus is a microorganism that replicates itself as a microRNA and infects the host cell. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Virus","biolink:Virus"]] = Field(["biolink:Virus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class CellularOrganism(OrganismalEntity, SubjectOfInvestigation): + + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CellularOrganism","biolink:CellularOrganism"]] = Field(["biolink:CellularOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Mammal(CellularOrganism, SubjectOfInvestigation): + """ + A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Mammal","biolink:Mammal"]] = Field(["biolink:Mammal"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Human(Mammal, SubjectOfInvestigation): + """ + A member of the the species Homo sapiens. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Human","biolink:Human"]] = Field(["biolink:Human"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Plant(CellularOrganism): + + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Plant","biolink:Plant"]] = Field(["biolink:Plant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Invertebrate(CellularOrganism): + """ + An animal lacking a vertebral column. This group consists of 98% of all animal species. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Invertebrate","biolink:Invertebrate"]] = Field(["biolink:Invertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Vertebrate(CellularOrganism): + """ + A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Vertebrate","biolink:Vertebrate"]] = Field(["biolink:Vertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Fungus(CellularOrganism): + """ + A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds). + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Fungus","biolink:Fungus"]] = Field(["biolink:Fungus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class LifeStage(OrganismalEntity): + """ + A stage of development or growth of an organism, including post-natal adult stages + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/LifeStage","biolink:LifeStage"]] = Field(["biolink:LifeStage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class IndividualOrganism(OrganismalEntity, SubjectOfInvestigation): + """ + An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576 + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/IndividualOrganism","biolink:IndividualOrganism"]] = Field(["biolink:IndividualOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class PopulationOfIndividualOrganisms(OrganismalEntity, SubjectOfInvestigation): + """ + A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PopulationOfIndividualOrganisms","biolink:PopulationOfIndividualOrganisms"]] = Field(["biolink:PopulationOfIndividualOrganisms"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class StudyPopulation(PopulationOfIndividualOrganisms): + """ + A group of people banded together or treated as a group as participants in a research study. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/StudyPopulation","biolink:StudyPopulation"]] = Field(["biolink:StudyPopulation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class DiseaseOrPhenotypicFeature(BiologicalEntity): + """ + Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature","biolink:DiseaseOrPhenotypicFeature"]] = Field(["biolink:DiseaseOrPhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Disease(DiseaseOrPhenotypicFeature): + """ + A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Disease","biolink:Disease"]] = Field(["biolink:Disease"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PhenotypicFeature(DiseaseOrPhenotypicFeature): + """ + A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicFeature","biolink:PhenotypicFeature"]] = Field(["biolink:PhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class BehavioralFeature(PhenotypicFeature): + """ + A phenotypic feature which is behavioral in nature. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/BehavioralFeature","biolink:BehavioralFeature"]] = Field(["biolink:BehavioralFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class AnatomicalEntity(OrganismalEntity, PhysicalEssence): + """ + A subcellular location, cell type or gross anatomical part + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntity","biolink:AnatomicalEntity"]] = Field(["biolink:AnatomicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class CellularComponent(AnatomicalEntity): + """ + A location in or around a cell + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CellularComponent","biolink:CellularComponent"]] = Field(["biolink:CellularComponent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Cell(AnatomicalEntity): + + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Cell","biolink:Cell"]] = Field(["biolink:Cell"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class CellLine(OrganismalEntity, SubjectOfInvestigation): + + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CellLine","biolink:CellLine"]] = Field(["biolink:CellLine"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class GrossAnatomicalStructure(AnatomicalEntity): + + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GrossAnatomicalStructure","biolink:GrossAnatomicalStructure"]] = Field(["biolink:GrossAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class ChemicalEntityOrGeneOrGeneProduct(ConfiguredBaseModel): + """ + A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities. + """ + None + + + +class RegulatoryRegion(ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): + """ + A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/RegulatoryRegion","biolink:RegulatoryRegion"]] = Field(["biolink:RegulatoryRegion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class AccessibleDnaRegion(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, PhysicalEssence, OntologyClass): + """ + A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/AccessibleDnaRegion","biolink:AccessibleDnaRegion"]] = Field(["biolink:AccessibleDnaRegion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class TranscriptionFactorBindingSite(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, PhysicalEssence, OntologyClass): + """ + A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/TranscriptionFactorBindingSite","biolink:TranscriptionFactorBindingSite"]] = Field(["biolink:TranscriptionFactorBindingSite"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalEntityOrProteinOrPolypeptide(ConfiguredBaseModel): + """ + A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities. + """ + None + + + +class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, NamedThing, ChemicalOrDrugOrTreatment): + """ + A chemical entity is a physical entity that pertains to chemistry or biochemistry. + """ + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntity","biolink:ChemicalEntity"]] = Field(["biolink:ChemicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MolecularEntity(ChemicalEntity): + """ + A molecular entity is a chemical entity composed of individual or covalently bonded atoms. + """ + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MolecularEntity","biolink:MolecularEntity"]] = Field(["biolink:MolecularEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SmallMolecule(MolecularEntity): + """ + A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion). + """ + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/SmallMolecule","biolink:SmallMolecule"]] = Field(["biolink:SmallMolecule"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalMixture(ChemicalEntity): + """ + A chemical mixture is a chemical entity composed of two or more molecular entities. + """ + is_supplement: Optional[str] = Field(None) + highest_FDA_approval_status: Optional[str] = Field(None, description="""Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'""") + drug_regulatory_status_world_wide: Optional[str] = Field(None, description="""An agglomeration of drug regulatory status worldwide. Not specific to FDA.""") + routes_of_delivery: Optional[List[DrugDeliveryEnum]] = Field(None, description="""the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalMixture","biolink:ChemicalMixture"]] = Field(["biolink:ChemicalMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, PhysicalEssence, OntologyClass): + """ + A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included. + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/NucleicAcidEntity","biolink:NucleicAcidEntity"]] = Field(["biolink:NucleicAcidEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MolecularMixture(ChemicalMixture): + """ + A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry. + """ + is_supplement: Optional[str] = Field(None) + highest_FDA_approval_status: Optional[str] = Field(None, description="""Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'""") + drug_regulatory_status_world_wide: Optional[str] = Field(None, description="""An agglomeration of drug regulatory status worldwide. Not specific to FDA.""") + routes_of_delivery: Optional[List[DrugDeliveryEnum]] = Field(None, description="""the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MolecularMixture","biolink:MolecularMixture"]] = Field(["biolink:MolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ComplexMolecularMixture(ChemicalMixture): + """ + A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry. + """ + is_supplement: Optional[str] = Field(None) + highest_FDA_approval_status: Optional[str] = Field(None, description="""Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'""") + drug_regulatory_status_world_wide: Optional[str] = Field(None, description="""An agglomeration of drug regulatory status worldwide. Not specific to FDA.""") + routes_of_delivery: Optional[List[DrugDeliveryEnum]] = Field(None, description="""the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ComplexMolecularMixture","biolink:ComplexMolecularMixture"]] = Field(["biolink:ComplexMolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ProcessedMaterial(ChemicalMixture): + """ + A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing. + """ + is_supplement: Optional[str] = Field(None) + highest_FDA_approval_status: Optional[str] = Field(None, description="""Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'""") + drug_regulatory_status_world_wide: Optional[str] = Field(None, description="""An agglomeration of drug regulatory status worldwide. Not specific to FDA.""") + routes_of_delivery: Optional[List[DrugDeliveryEnum]] = Field(None, description="""the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ProcessedMaterial","biolink:ProcessedMaterial"]] = Field(["biolink:ProcessedMaterial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): + """ + A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease + """ + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_supplement: Optional[str] = Field(None) + highest_FDA_approval_status: Optional[str] = Field(None, description="""Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'""") + drug_regulatory_status_world_wide: Optional[str] = Field(None, description="""An agglomeration of drug regulatory status worldwide. Not specific to FDA.""") + routes_of_delivery: Optional[List[DrugDeliveryEnum]] = Field(None, description="""the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Drug","biolink:Drug"]] = Field(["biolink:Drug"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EnvironmentalFoodContaminant(ChemicalEntity): + + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFoodContaminant","biolink:EnvironmentalFoodContaminant"]] = Field(["biolink:EnvironmentalFoodContaminant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class FoodAdditive(ChemicalEntity): + + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/FoodAdditive","biolink:FoodAdditive"]] = Field(["biolink:FoodAdditive"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Food(ChemicalMixture): + """ + A substance consumed by a living organism as a source of nutrition + """ + is_supplement: Optional[str] = Field(None) + highest_FDA_approval_status: Optional[str] = Field(None, description="""Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'""") + drug_regulatory_status_world_wide: Optional[str] = Field(None, description="""An agglomeration of drug regulatory status worldwide. Not specific to FDA.""") + routes_of_delivery: Optional[List[DrugDeliveryEnum]] = Field(None, description="""the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Food","biolink:Food"]] = Field(["biolink:Food"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MacromolecularMachineMixin(ConfiguredBaseModel): + """ + A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this. + """ + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + + + +class GeneOrGeneProduct(MacromolecularMachineMixin): + """ + A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another + """ + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + + + +class Gene(GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): + """ + A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions. + """ + symbol: Optional[str] = Field(None, description="""Symbol for a particular thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Gene","biolink:Gene"]] = Field(["biolink:Gene"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneProductMixin(GeneOrGeneProduct): + """ + The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules. + """ + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + + + +class GeneProductIsoformMixin(GeneProductMixin): + """ + This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms. + """ + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + + + +class MacromolecularComplex(MacromolecularMachineMixin, BiologicalEntity): + """ + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + """ + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularComplex","biolink:MacromolecularComplex"]] = Field(["biolink:MacromolecularComplex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class NucleosomeModification(GeneProductIsoformMixin, EpigenomicEntity, GenomicEntity, BiologicalEntity): + """ + A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A. + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/NucleosomeModification","biolink:NucleosomeModification"]] = Field(["biolink:NucleosomeModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + + + +class Genome(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): + """ + A genome is the sum of genetic material within a cell or virion. + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Genome","biolink:Genome"]] = Field(["biolink:Genome"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Exon(NucleicAcidEntity): + """ + A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Exon","biolink:Exon"]] = Field(["biolink:Exon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Transcript(NucleicAcidEntity): + """ + An RNA synthesized on a DNA or RNA template by an RNA polymerase. + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Transcript","biolink:Transcript"]] = Field(["biolink:Transcript"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class CodingSequence(NucleicAcidEntity): + + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CodingSequence","biolink:CodingSequence"]] = Field(["biolink:CodingSequence"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Polypeptide(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGeneProduct, BiologicalEntity): + """ + A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Polypeptide","biolink:Polypeptide"]] = Field(["biolink:Polypeptide"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Protein(Polypeptide, GeneProductMixin): + """ + A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA + """ + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Protein","biolink:Protein"]] = Field(["biolink:Protein"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ProteinIsoform(Protein, GeneProductIsoformMixin): + """ + Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ + """ + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ProteinIsoform","biolink:ProteinIsoform"]] = Field(["biolink:ProteinIsoform"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PosttranslationalModification(GeneProductIsoformMixin, BiologicalEntity): + """ + A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PosttranslationalModification","biolink:PosttranslationalModification"]] = Field(["biolink:PosttranslationalModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + + + +class NucleicAcidSequenceMotif(BiologicalEntity): + """ + A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/NucleicAcidSequenceMotif","biolink:NucleicAcidSequenceMotif"]] = Field(["biolink:NucleicAcidSequenceMotif"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class RNAProduct(Transcript, GeneProductMixin): + + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/RNAProduct","biolink:RNAProduct"]] = Field(["biolink:RNAProduct"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): + """ + Represents a protein that is a specific isoform of the canonical or reference RNA + """ + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/RNAProductIsoform","biolink:RNAProductIsoform"]] = Field(["biolink:RNAProductIsoform"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class NoncodingRNAProduct(RNAProduct): + + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/NoncodingRNAProduct","biolink:NoncodingRNAProduct"]] = Field(["biolink:NoncodingRNAProduct"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MicroRNA(NoncodingRNAProduct): + + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MicroRNA","biolink:MicroRNA"]] = Field(["biolink:MicroRNA"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SiRNA(NoncodingRNAProduct): + """ + A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. + """ + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + is_metabolite: Optional[bool] = Field(None, description="""indicates whether a molecular entity is a metabolite""") + trade_name: Optional[str] = Field(None) + available_from: Optional[List[DrugAvailabilityEnum]] = Field(None) + max_tolerated_dose: Optional[str] = Field(None, description="""The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.""") + is_toxic: Optional[bool] = Field(None) + has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/SiRNA","biolink:SiRNA"]] = Field(["biolink:SiRNA"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneGroupingMixin(ConfiguredBaseModel): + """ + any grouping of multiple genes or gene products + """ + has_gene_or_gene_product: Optional[List[str]] = Field(None, description="""connects an entity with one or more gene or gene products""") + + + +class ProteinDomain(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, BiologicalEntity): + """ + A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain. + """ + has_gene_or_gene_product: Optional[List[str]] = Field(None, description="""connects an entity with one or more gene or gene products""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ProteinDomain","biolink:ProteinDomain"]] = Field(["biolink:ProteinDomain"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ProteinFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, BiologicalEntity): + + has_gene_or_gene_product: Optional[List[str]] = Field(None, description="""connects an entity with one or more gene or gene products""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ProteinFamily","biolink:ProteinFamily"]] = Field(["biolink:ProteinFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, BiologicalEntity): + """ + any grouping of multiple genes or gene products related by common descent + """ + has_gene_or_gene_product: Optional[List[str]] = Field(None, description="""connects an entity with one or more gene or gene products""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneFamily","biolink:GeneFamily"]] = Field(["biolink:GeneFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Zygosity(Attribute): + + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/Zygosity","biolink:Zygosity"]] = Field(["biolink:Zygosity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Genotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): + """ + An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background + """ + has_zygosity: Optional[str] = Field(None) + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Genotype","biolink:Genotype"]] = Field(["biolink:Genotype"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Haplotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): + """ + A set of zero or more Alleles on a single instance of a Sequence[VMC] + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Haplotype","biolink:Haplotype"]] = Field(["biolink:Haplotype"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SequenceVariant(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): + """ + A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. + """ + has_gene: Optional[List[str]] = Field(None, description="""Each allele can be associated with any number of genes""") + has_biological_sequence: Optional[str] = Field(None, description="""The state of the sequence w.r.t a reference sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/SequenceVariant","biolink:SequenceVariant"]] = Field(["biolink:SequenceVariant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Snv(SequenceVariant): + """ + SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist + """ + has_gene: Optional[List[str]] = Field(None, description="""Each allele can be associated with any number of genes""") + has_biological_sequence: Optional[str] = Field(None, description="""The state of the sequence w.r.t a reference sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Snv","biolink:Snv"]] = Field(["biolink:Snv"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ReagentTargetedGene(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): + """ + A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. + """ + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ReagentTargetedGene","biolink:ReagentTargetedGene"]] = Field(["biolink:ReagentTargetedGene"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ClinicalAttribute(Attribute): + """ + Attributes relating to a clinical manifestation + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/ClinicalAttribute","biolink:ClinicalAttribute"]] = Field(["biolink:ClinicalAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ClinicalMeasurement(ClinicalAttribute): + """ + A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot. + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/ClinicalMeasurement","biolink:ClinicalMeasurement"]] = Field(["biolink:ClinicalMeasurement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ClinicalModifier(ClinicalAttribute): + """ + Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/ClinicalModifier","biolink:ClinicalModifier"]] = Field(["biolink:ClinicalModifier"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ClinicalCourse(ClinicalAttribute): + """ + The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/ClinicalCourse","biolink:ClinicalCourse"]] = Field(["biolink:ClinicalCourse"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Onset(ClinicalCourse): + """ + The age group in which (disease) symptom manifestations appear + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/Onset","biolink:Onset"]] = Field(["biolink:Onset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ClinicalEntity(NamedThing): + """ + Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities + """ + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ClinicalEntity","biolink:ClinicalEntity"]] = Field(["biolink:ClinicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ClinicalTrial(ClinicalEntity): + + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ClinicalTrial","biolink:ClinicalTrial"]] = Field(["biolink:ClinicalTrial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ClinicalIntervention(ClinicalEntity): + + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ClinicalIntervention","biolink:ClinicalIntervention"]] = Field(["biolink:ClinicalIntervention"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ClinicalFinding(PhenotypicFeature): + """ + this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ClinicalFinding","biolink:ClinicalFinding"]] = Field(["biolink:ClinicalFinding"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Hospitalization(ClinicalIntervention): + + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Hospitalization","biolink:Hospitalization"]] = Field(["biolink:Hospitalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SocioeconomicAttribute(Attribute): + """ + Attributes relating to a socioeconomic manifestation + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicAttribute","biolink:SocioeconomicAttribute"]] = Field(["biolink:SocioeconomicAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Case(IndividualOrganism, SubjectOfInvestigation): + """ + An individual (human) organism that has a patient role in some clinical context. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Case","biolink:Case"]] = Field(["biolink:Case"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class Cohort(StudyPopulation, SubjectOfInvestigation): + """ + A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Cohort","biolink:Cohort"]] = Field(["biolink:Cohort"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class ExposureEvent(OntologyClass): + """ + A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + + + +class GenomicBackgroundExposure(ExposureEvent, GeneGroupingMixin, GenomicEntity, ThingWithTaxon, PhysicalEssence, Attribute, OntologyClass): + """ + A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome. + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + has_gene_or_gene_product: Optional[List[str]] = Field(None, description="""connects an entity with one or more gene or gene products""") + has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/GenomicBackgroundExposure","biolink:GenomicBackgroundExposure"]] = Field(["biolink:GenomicBackgroundExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PathologicalEntityMixin(ConfiguredBaseModel): + """ + A pathological (abnormal) structure or process. + """ + None + + + +class PathologicalProcess(PathologicalEntityMixin, BiologicalProcess): + """ + A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. + """ + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + has_input: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an input into the process""") + has_output: Optional[List[str]] = Field(None, description="""holds between a process and a continuant, where the continuant is an output of the process""") + enabled_by: Optional[List[str]] = Field(None, description="""holds between a process and a physical entity, where the physical entity executes the process""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PathologicalProcess","biolink:PathologicalProcess"]] = Field(["biolink:PathologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PathologicalProcessExposure(ExposureEvent, Attribute): + """ + A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease. + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/PathologicalProcessExposure","biolink:PathologicalProcessExposure"]] = Field(["biolink:PathologicalProcessExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PathologicalAnatomicalStructure(PathologicalEntityMixin, AnatomicalEntity): + """ + An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. + """ + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalStructure","biolink:PathologicalAnatomicalStructure"]] = Field(["biolink:PathologicalAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") + + + +class PathologicalAnatomicalExposure(ExposureEvent, Attribute): + """ + An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome. + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalExposure","biolink:PathologicalAnatomicalExposure"]] = Field(["biolink:PathologicalAnatomicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DiseaseOrPhenotypicFeatureExposure(PathologicalEntityMixin, ExposureEvent, Attribute): + """ + A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer. + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureExposure","biolink:DiseaseOrPhenotypicFeatureExposure"]] = Field(["biolink:DiseaseOrPhenotypicFeatureExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalExposure(ExposureEvent, Attribute): + """ + A chemical exposure is an intake of a particular chemical entity. + """ + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalExposure","biolink:ChemicalExposure"]] = Field(["biolink:ChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ComplexChemicalExposure(Attribute): + """ + A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. + """ + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/ComplexChemicalExposure","biolink:ComplexChemicalExposure"]] = Field(["biolink:ComplexChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DrugExposure(ChemicalExposure, ExposureEvent): + """ + A drug exposure is an intake of a particular drug. + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/DrugExposure","biolink:DrugExposure"]] = Field(["biolink:DrugExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DrugToGeneInteractionExposure(DrugExposure, GeneGroupingMixin): + """ + drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome. + """ + has_gene_or_gene_product: Optional[List[str]] = Field(None, description="""connects an entity with one or more gene or gene products""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/DrugToGeneInteractionExposure","biolink:DrugToGeneInteractionExposure"]] = Field(["biolink:DrugToGeneInteractionExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class Treatment(ExposureEvent, NamedThing, ChemicalOrDrugOrTreatment): + """ + A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures + """ + has_drug: Optional[List[str]] = Field(None, description="""connects an entity to one or more drugs""") + has_device: Optional[List[str]] = Field(None, description="""connects an entity to one or more (medical) devices""") + has_procedure: Optional[List[str]] = Field(None, description="""connects an entity to one or more (medical) procedures""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Treatment","biolink:Treatment"]] = Field(["biolink:Treatment"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class BioticExposure(ExposureEvent, Attribute): + """ + An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/BioticExposure","biolink:BioticExposure"]] = Field(["biolink:BioticExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EnvironmentalExposure(ExposureEvent, Attribute): + """ + A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants. + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalExposure","biolink:EnvironmentalExposure"]] = Field(["biolink:EnvironmentalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeographicExposure(EnvironmentalExposure, ExposureEvent): + """ + A geographic exposure is a factor relating to geographic proximity to some impactful entity. + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeographicExposure","biolink:GeographicExposure"]] = Field(["biolink:GeographicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class BehavioralExposure(ExposureEvent, Attribute): + """ + A behavioral exposure is a factor relating to behavior impacting an individual. + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/BehavioralExposure","biolink:BehavioralExposure"]] = Field(["biolink:BehavioralExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SocioeconomicExposure(ExposureEvent, Attribute): + """ + A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty). + """ + timepoint: Optional[str] = Field(None, description="""a point in time""") + name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") + has_attribute_type: str = Field(..., description="""connects an attribute to a class that describes it""") + has_quantitative_value: Optional[List[QuantityValue]] = Field(None, description="""connects an attribute to a value""") + has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicExposure","biolink:SocioeconomicExposure"]] = Field(["biolink:SocioeconomicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + description: Optional[str] = Field(None) + has_attribute: List[str] = Field(..., description="""connects any entity to an attribute""") + + + +class Outcome(ConfiguredBaseModel): + """ + An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes. + """ + None + + + +class PathologicalProcessOutcome(Outcome): + """ + An outcome resulting from an exposure event which is the manifestation of a pathological process. + """ + None + + + +class PathologicalAnatomicalOutcome(Outcome): + """ + An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure. + """ + None + + + +class DiseaseOrPhenotypicFeatureOutcome(Outcome): + """ + Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype. + """ + None + + + +class BehavioralOutcome(Outcome): + """ + An outcome resulting from an exposure event which is the manifestation of human behavior. + """ + None + + + +class HospitalizationOutcome(Outcome): + """ + An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization. + """ + None + + + +class MortalityOutcome(Outcome): + """ + An outcome of death from resulting from an exposure event. + """ + None + + + +class EpidemiologicalOutcome(Outcome): + """ + An epidemiological outcome, such as societal disease burden, resulting from an exposure event. + """ + None + + + +class SocioeconomicOutcome(Outcome): + """ + An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event + """ + None + + + +class Association(Entity): + """ + A typed association between two entities, supported by evidence + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/Association","biolink:Association"]] = Field(["biolink:Association"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalEntityAssessesNamedThingAssociation(Association): + + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntityAssessesNamedThingAssociation","biolink:ChemicalEntityAssessesNamedThingAssociation"]] = Field(["biolink:ChemicalEntityAssessesNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ContributorAssociation(Association): + """ + Any association between an entity (such as a publication) and various agents that contribute to its realisation + """ + subject: str = Field(..., description="""information content entity which an agent has helped realise""") + predicate: str = Field(..., description="""generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'""") + object: str = Field(..., description="""agent helping to realise the given entity (e.g. such as a publication)""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ContributorAssociation","biolink:ContributorAssociation"]] = Field(["biolink:ContributorAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GenotypeToGenotypePartAssociation(Association): + """ + Any association between one genotype and a genotypic entity that is a sub-component of it + """ + subject: str = Field(..., description="""parent genotype""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""child genotype""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToGenotypePartAssociation","biolink:GenotypeToGenotypePartAssociation"]] = Field(["biolink:GenotypeToGenotypePartAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GenotypeToGeneAssociation(Association): + """ + Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality + """ + subject: str = Field(..., description="""parent genotype""") + predicate: str = Field(..., description="""the relationship type used to connect genotype to gene""") + object: str = Field(..., description="""gene implicated in genotype""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToGeneAssociation","biolink:GenotypeToGeneAssociation"]] = Field(["biolink:GenotypeToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GenotypeToVariantAssociation(Association): + """ + Any association between a genotype and a sequence variant. + """ + subject: str = Field(..., description="""parent genotype""") + predicate: str = Field(..., description="""the relationship type used to connect genotype to gene""") + object: str = Field(..., description="""gene implicated in genotype""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToVariantAssociation","biolink:GenotypeToVariantAssociation"]] = Field(["biolink:GenotypeToVariantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneToGeneAssociation(Association): + """ + abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction. + """ + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneAssociation","biolink:GeneToGeneAssociation"]] = Field(["biolink:GeneToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneToGeneHomologyAssociation(GeneToGeneAssociation): + """ + A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same) + """ + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""homology relationship type""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneHomologyAssociation","biolink:GeneToGeneHomologyAssociation"]] = Field(["biolink:GeneToGeneHomologyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneToGeneFamilyAssociation(Association): + """ + Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships. + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""membership of the gene in the given gene family.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneFamilyAssociation","biolink:GeneToGeneFamilyAssociation"]] = Field(["biolink:GeneToGeneFamilyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneExpressionMixin(ConfiguredBaseModel): + """ + Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs. + """ + quantifier_qualifier: Optional[str] = Field(None, description="""Optional quantitative value indicating degree of expression.""") + expression_site: Optional[str] = Field(None, description="""location in which gene or protein expression takes place. May be cell, tissue, or organ.""") + stage_qualifier: Optional[str] = Field(None, description="""stage during which gene or protein expression of takes place.""") + phenotypic_state: Optional[str] = Field(None, description="""in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.""") + + + +class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociation): + """ + Indicates that two genes are co-expressed, generally under the same conditions. + """ + quantifier_qualifier: Optional[str] = Field(None, description="""Optional quantitative value indicating degree of expression.""") + expression_site: Optional[str] = Field(None, description="""location in which gene or protein expression takes place. May be cell, tissue, or organ.""") + stage_qualifier: Optional[str] = Field(None, description="""stage during which gene or protein expression of takes place.""") + phenotypic_state: Optional[str] = Field(None, description="""in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.""") + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneCoexpressionAssociation","biolink:GeneToGeneCoexpressionAssociation"]] = Field(["biolink:GeneToGeneCoexpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): + """ + An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation) + """ + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""interaction relationship type""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PairwiseGeneToGeneInteraction","biolink:PairwiseGeneToGeneInteraction"]] = Field(["biolink:PairwiseGeneToGeneInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): + """ + An interaction at the molecular level between two physical entities + """ + interacting_molecules_category: Optional[str] = Field(None) + subject: str = Field(..., description="""the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + predicate: str = Field(..., description="""interaction relationship type""") + object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""identifier for the interaction. This may come from an interaction database such as IMEX.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PairwiseMolecularInteraction","biolink:PairwiseMolecularInteraction"]] = Field(["biolink:PairwiseMolecularInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class CellLineToEntityAssociationMixin(ConfiguredBaseModel): + """ + An relationship between a cell line and another entity + """ + None + + + +class ChemicalEntityToEntityAssociationMixin(ConfiguredBaseModel): + """ + An interaction between a chemical entity and another entity + """ + None + + + +class DrugToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): + """ + An interaction between a drug and another entity + """ + None + + + +class ChemicalToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): + """ + An interaction between a chemical entity and another entity + """ + None + + + +class CaseToEntityAssociationMixin(ConfiguredBaseModel): + """ + An abstract association for use where the case is the subject + """ + None + + + +class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Association): + """ + A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another. + """ + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the chemical element that is the target of the statement""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToChemicalAssociation","biolink:ChemicalToChemicalAssociation"]] = Field(["biolink:ChemicalToChemicalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): + + stoichiometry: Optional[int] = Field(None, description="""the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.""") + reaction_direction: Optional[ReactionDirectionEnum] = Field(None, description="""the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)""") + reaction_side: Optional[ReactionSideEnum] = Field(None, description="""the side of a reaction being modeled (ie: left or right)""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the chemical element that is the target of the statement""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ReactionToParticipantAssociation","biolink:ReactionToParticipantAssociation"]] = Field(["biolink:ReactionToParticipantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ReactionToCatalystAssociation(ReactionToParticipantAssociation): + + stoichiometry: Optional[int] = Field(None, description="""the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.""") + reaction_direction: Optional[ReactionDirectionEnum] = Field(None, description="""the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)""") + reaction_side: Optional[ReactionSideEnum] = Field(None, description="""the side of a reaction being modeled (ie: left or right)""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the chemical element that is the target of the statement""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ReactionToCatalystAssociation","biolink:ReactionToCatalystAssociation"]] = Field(["biolink:ReactionToCatalystAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): + """ + A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: + IF + R has-input C1 AND + R has-output C2 AND + R enabled-by P AND + R type Reaction + THEN + C1 derives-into C2 <> + """ + catalyst_qualifier: Optional[List[str]] = Field(None, description="""this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.""") + subject: str = Field(..., description="""the upstream chemical entity""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the downstream chemical entity""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToChemicalDerivationAssociation","biolink:ChemicalToChemicalDerivationAssociation"]] = Field(["biolink:ChemicalToChemicalDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MolecularActivityToPathwayAssociation(Association): + """ + Association that holds the relationship between a reaction and the pathway it participates in. + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToPathwayAssociation","biolink:MolecularActivityToPathwayAssociation"]] = Field(["biolink:MolecularActivityToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association): + """ + An interaction between a chemical entity and a biological process or pathway. + """ + subject: str = Field(..., description="""the chemical entity that is affecting the pathway""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the pathway that is affected by the chemical""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToPathwayAssociation","biolink:ChemicalToPathwayAssociation"]] = Field(["biolink:ChemicalToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): + + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/NamedThingAssociatedWithLikelihoodOfNamedThingAssociation","biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"]] = Field(["biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Association): + """ + describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction) + """ + subject_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormOrVariantEnum] = Field(None) + subject_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + subject_derivative_qualifier: Optional[ChemicalEntityDerivativeEnum] = Field(None) + subject_context_qualifier: Optional[str] = Field(None) + object_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormOrVariantEnum] = Field(None) + object_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + object_context_qualifier: Optional[str] = Field(None) + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalGeneInteractionAssociation","biolink:ChemicalGeneInteractionAssociation"]] = Field(["biolink:ChemicalGeneInteractionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalAffectsGeneAssociation(Association): + """ + Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.) + """ + subject_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormOrVariantEnum] = Field(None) + subject_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + subject_derivative_qualifier: Optional[ChemicalEntityDerivativeEnum] = Field(None) + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + subject_context_qualifier: Optional[str] = Field(None) + subject_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + object_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormOrVariantEnum] = Field(None) + object_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + object_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + object_context_qualifier: Optional[str] = Field(None) + causal_mechanism_qualifier: Optional[CausalMechanismQualifierEnum] = Field(None, description="""A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") + qualified_predicate: Optional[str] = Field(None, description="""Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalAffectsGeneAssociation","biolink:ChemicalAffectsGeneAssociation"]] = Field(["biolink:ChemicalAffectsGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): + """ + An interaction between a drug and a gene or gene product. + """ + subject: str = Field(..., description="""the drug that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the gene or gene product that is affected by the drug""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DrugToGeneAssociation","biolink:DrugToGeneAssociation"]] = Field(["biolink:DrugToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MaterialSampleToEntityAssociationMixin(ConfiguredBaseModel): + """ + An association between a material sample and something. + """ + None + + + +class MaterialSampleDerivationAssociation(Association): + """ + An association between a material sample and the material entity from which it is derived. + """ + subject: str = Field(..., description="""the material sample being described""") + predicate: str = Field(..., description="""derivation relationship""") + object: str = Field(..., description="""the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MaterialSampleDerivationAssociation","biolink:MaterialSampleDerivationAssociation"]] = Field(["biolink:MaterialSampleDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DiseaseToEntityAssociationMixin(ConfiguredBaseModel): + + None + + + +class EntityToExposureEventAssociationMixin(ConfiguredBaseModel): + """ + An association between some entity and an exposure event. + """ + None + + + +class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, DiseaseToEntityAssociationMixin, Association): + """ + An association between an exposure event and a disease. + """ + subject: str = Field(..., description="""disease class""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DiseaseToExposureEventAssociation","biolink:DiseaseToExposureEventAssociation"]] = Field(["biolink:DiseaseToExposureEventAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EntityToOutcomeAssociationMixin(ConfiguredBaseModel): + """ + An association between some entity and an outcome + """ + None + + + +class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Association): + """ + An association between an exposure event and an outcome. + """ + population_context_qualifier: Optional[str] = Field(None, description="""a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.""") + temporal_context_qualifier: Optional[str] = Field(None, description="""a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ExposureEventToOutcomeAssociation","biolink:ExposureEventToOutcomeAssociation"]] = Field(["biolink:ExposureEventToOutcomeAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class FrequencyQualifierMixin(ConfiguredBaseModel): + """ + Qualifier for frequency type associations + """ + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class EntityToFeatureOrDiseaseQualifiersMixin(FrequencyQualifierMixin): + """ + Qualifiers for entity to disease or phenotype associations. + """ + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class EntityToPhenotypicFeatureAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin, FrequencyQuantifier): + + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class InformationContentEntityToNamedThingAssociation(Association): + """ + association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property). + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/InformationContentEntityToNamedThingAssociation","biolink:InformationContentEntityToNamedThingAssociation"]] = Field(["biolink:InformationContentEntityToNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EntityToDiseaseAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin): + """ + mixin class for any association whose object (target node) is a disease + """ + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class DiseaseOrPhenotypicFeatureToEntityAssociationMixin(ConfiguredBaseModel): + + None + + + +class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeatureToEntityAssociationMixin, Association): + """ + An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site. + """ + subject: str = Field(..., description="""disease or phenotype""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""anatomical entity in which the disease or feature is found.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToLocationAssociation","biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"]] = Field(["biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenotypicFeatureToEntityAssociationMixin, Association): + """ + An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. + """ + subject: str = Field(..., description="""disease or phenotype""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""genetic inheritance associated with the specified disease or phenotypic feature.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation","biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"]] = Field(["biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EntityToDiseaseOrPhenotypicFeatureAssociationMixin(ConfiguredBaseModel): + + None + + + +class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypicFeatureAssociationMixin, CellLineToEntityAssociationMixin, Association): + """ + An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype. + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease or phenotype""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CellLineToDiseaseOrPhenotypicFeatureAssociation","biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypicFeatureAssociationMixin, ChemicalToEntityAssociationMixin, Association): + """ + An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype. + """ + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the disease or phenotype that is affected by the chemical""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypicFeatureAssociationMixin, ChemicalToEntityAssociationMixin, Association): + """ + This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect. + """ + FDA_adverse_event_level: Optional[FDAIDAAdverseEventEnum] = Field(None) + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease or phenotype""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation, EntityToDiseaseOrPhenotypicFeatureAssociationMixin, ChemicalToEntityAssociationMixin): + """ + This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect. + """ + FDA_adverse_event_level: Optional[FDAIDAAdverseEventEnum] = Field(None) + subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease or phenotype""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypicFeatureAssociationMixin, MaterialSampleToEntityAssociationMixin, Association): + """ + An association between a material sample and a disease or phenotype. + """ + subject: str = Field(..., description="""the material sample being described""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease or phenotype""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MaterialSampleToDiseaseOrPhenotypicFeatureAssociation","biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GenotypeToEntityAssociationMixin(ConfiguredBaseModel): + + None + + + +class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, Association): + """ + Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment + """ + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""genotype that is associated with the phenotypic feature""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToPhenotypicFeatureAssociation","biolink:GenotypeToPhenotypicFeatureAssociation"]] = Field(["biolink:GenotypeToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMixin, Association): + """ + Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype. + """ + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ExposureEventToPhenotypicFeatureAssociation","biolink:ExposureEventToPhenotypicFeatureAssociation"]] = Field(["biolink:ExposureEventToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMixin, DiseaseToEntityAssociationMixin, Association): + """ + An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way. + """ + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""disease class""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DiseaseToPhenotypicFeatureAssociation","biolink:DiseaseToPhenotypicFeatureAssociation"]] = Field(["biolink:DiseaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMixin, CaseToEntityAssociationMixin, Association): + """ + An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype. + """ + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""the case (e.g. patient) that has the property""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CaseToPhenotypicFeatureAssociation","biolink:CaseToPhenotypicFeatureAssociation"]] = Field(["biolink:CaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociationMixin, Association): + """ + An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior. + """ + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""behavior that is the subject of the association""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""behavioral feature that is the object of the association""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/BehaviorToBehavioralFeatureAssociation","biolink:BehaviorToBehavioralFeatureAssociation"]] = Field(["biolink:BehaviorToBehavioralFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class GeneToEntityAssociationMixin(ConfiguredBaseModel): + + None + + + +class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): + """ + An interaction between a gene or gene product and a biological process or pathway. + """ + subject: str = Field(..., description="""the gene or gene product entity that participates or influences the pathway""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the pathway that includes or is affected by the gene or gene product""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToPathwayAssociation","biolink:GeneToPathwayAssociation"]] = Field(["biolink:GeneToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class VariantToEntityAssociationMixin(ConfiguredBaseModel): + + None + + + +class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, Association): + + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""gene in which variation is correlated with the phenotypic feature""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation","biolink:GeneToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:GeneToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class GeneToPhenotypeAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin): + + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + subject: str = Field(..., description="""gene in which variation is correlated with the phenotypic feature""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToPhenotypeAssociation","biolink:GeneToPhenotypeAssociation"]] = Field(["biolink:GeneToPhenotypeAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): + + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToDiseaseAssociation","biolink:GeneToDiseaseAssociation"]] = Field(["biolink:GeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): + + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""gene in which variation is shown to cause the disease.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation","biolink:CausalGeneToDiseaseAssociation"]] = Field(["biolink:CausalGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): + + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""gene in which variation is shown to correlate with the disease.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation","biolink:CorrelatedGeneToDiseaseAssociation"]] = Field(["biolink:CorrelatedGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): + + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[DruggableGeneCategoryEnum]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/DruggableGeneToDiseaseAssociation","biolink:DruggableGeneToDiseaseAssociation"]] = Field(["biolink:DruggableGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): + """ + An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium) + """ + subject: str = Field(..., description="""a sequence variant in which the allele state is associated with some other entity""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/VariantToGeneAssociation","biolink:VariantToGeneAssociation"]] = Field(["biolink:VariantToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressionMixin): + """ + An association between a variant and expression of a gene (i.e. e-QTL) + """ + quantifier_qualifier: Optional[str] = Field(None, description="""Optional quantitative value indicating degree of expression.""") + expression_site: Optional[str] = Field(None, description="""location in which gene or protein expression takes place. May be cell, tissue, or organ.""") + stage_qualifier: Optional[str] = Field(None, description="""stage during which gene or protein expression of takes place.""") + phenotypic_state: Optional[str] = Field(None, description="""in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.""") + subject: str = Field(..., description="""a sequence variant in which the allele state is associated with some other entity""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/VariantToGeneExpressionAssociation","biolink:VariantToGeneExpressionAssociation"]] = Field(["biolink:VariantToGeneExpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQualifierMixin, Association, FrequencyQuantifier): + """ + An association between a variant and a population, where the variant has particular frequency in the population + """ + has_count: Optional[int] = Field(None, description="""number in object population that carry a particular allele, aka allele count""") + has_total: Optional[int] = Field(None, description="""number all populations that carry a particular allele, aka allele number""") + has_quotient: Optional[float] = Field(None, description="""frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency""") + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + subject: str = Field(..., description="""an allele that has a certain frequency in a given population""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the population that is observed to have the frequency""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/VariantToPopulationAssociation","biolink:VariantToPopulationAssociation"]] = Field(["biolink:VariantToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class PopulationToPopulationAssociation(Association): + """ + An association between a two populations + """ + subject: str = Field(..., description="""the population that form the subject of the association""") + predicate: str = Field(..., description="""A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used""") + object: str = Field(..., description="""the population that form the object of the association""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/PopulationToPopulationAssociation","biolink:PopulationToPopulationAssociation"]] = Field(["biolink:PopulationToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, Association): + + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""a sequence variant in which the allele state is associated in some way with the phenotype state""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/VariantToPhenotypicFeatureAssociation","biolink:VariantToPhenotypicFeatureAssociation"]] = Field(["biolink:VariantToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDiseaseAssociationMixin, Association): + + subject: str = Field(..., description="""a sequence variant in which the allele state is associated in some way with the disease state""") + predicate: str = Field(..., description="""E.g. is pathogenic for""") + object: str = Field(..., description="""a disease that is associated with that variant""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/VariantToDiseaseAssociation","biolink:VariantToDiseaseAssociation"]] = Field(["biolink:VariantToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDiseaseAssociationMixin, Association): + + subject: str = Field(..., description="""a genotype that is associated in some way with a disease state""") + predicate: str = Field(..., description="""E.g. is pathogenic for""") + object: str = Field(..., description="""a disease that is associated with that genotype""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToDiseaseAssociation","biolink:GenotypeToDiseaseAssociation"]] = Field(["biolink:GenotypeToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class ModelToDiseaseAssociationMixin(ConfiguredBaseModel): + """ + This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease + """ + None + + + +class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDiseaseAssociation, EntityToDiseaseAssociationMixin): + + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneAsAModelOfDiseaseAssociation","biolink:GeneAsAModelOfDiseaseAssociation"]] = Field(["biolink:GeneAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, VariantToDiseaseAssociation, EntityToDiseaseAssociationMixin): + + subject: str = Field(..., description="""A variant that has a role in modeling the disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/VariantAsAModelOfDiseaseAssociation","biolink:VariantAsAModelOfDiseaseAssociation"]] = Field(["biolink:VariantAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GenotypeToDiseaseAssociation, EntityToDiseaseAssociationMixin): + + subject: str = Field(..., description="""A genotype that has a role in modeling the disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GenotypeAsAModelOfDiseaseAssociation","biolink:GenotypeAsAModelOfDiseaseAssociation"]] = Field(["biolink:GenotypeAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellLineToDiseaseOrPhenotypicFeatureAssociation, EntityToDiseaseAssociationMixin): + + subject: str = Field(..., description="""A cell line derived from an organismal entity with a disease state that is used as a model of that disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/CellLineAsAModelOfDiseaseAssociation","biolink:CellLineAsAModelOfDiseaseAssociation"]] = Field(["biolink:CellLineAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, EntityToDiseaseAssociationMixin, Association): + + subject: str = Field(..., description="""A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.""") + predicate: str = Field(..., description="""The relationship to the disease""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/OrganismalEntityAsAModelOfDiseaseAssociation","biolink:OrganismalEntityAsAModelOfDiseaseAssociation"]] = Field(["biolink:OrganismalEntityAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class OrganismToOrganismAssociation(Association): + + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""An association between two individual organisms.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/OrganismToOrganismAssociation","biolink:OrganismToOrganismAssociation"]] = Field(["biolink:OrganismToOrganismAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class TaxonToTaxonAssociation(Association): + + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""An association between individuals of different taxa.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/TaxonToTaxonAssociation","biolink:TaxonToTaxonAssociation"]] = Field(["biolink:TaxonToTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation): + + subject_form_or_variant_qualifier: Optional[str] = Field(None) + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") + subject: str = Field(..., description="""A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""disease""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneHasVariantThatContributesToDiseaseAssociation","biolink:GeneHasVariantThatContributesToDiseaseAssociation"]] = Field(["biolink:GeneHasVariantThatContributesToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + has_count: Optional[int] = Field(None, description="""number of things with a particular property""") + has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") + has_quotient: Optional[float] = Field(None) + has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") + severity_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how severe the phenotype is in the subject""") + onset_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state when the phenotype appears is in the subject""") + frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") + + + +class GeneToExpressionSiteAssociation(Association): + """ + An association between a gene and a gene expression site, possibly qualified by stage/timing info. + """ + stage_qualifier: Optional[str] = Field(None, description="""stage at which the gene is expressed in the site""") + quantifier_qualifier: Optional[str] = Field(None, description="""can be used to indicate magnitude, or also ranking""") + subject: str = Field(..., description="""Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location.""") + predicate: str = Field(..., description="""expression relationship""") + object: str = Field(..., description="""location in which the gene is expressed""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToExpressionSiteAssociation","biolink:GeneToExpressionSiteAssociation"]] = Field(["biolink:GeneToExpressionSiteAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SequenceVariantModulatesTreatmentAssociation(Association): + """ + An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used. + """ + subject: str = Field(..., description="""variant that modulates the treatment of some disease""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""treatment whose efficacy is modulated by the subject variant""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/SequenceVariantModulatesTreatmentAssociation","biolink:SequenceVariantModulatesTreatmentAssociation"]] = Field(["biolink:SequenceVariantModulatesTreatmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class FunctionalAssociation(Association): + """ + An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed. + """ + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/FunctionalAssociation","biolink:FunctionalAssociation"]] = Field(["biolink:FunctionalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MacromolecularMachineToEntityAssociationMixin(ConfiguredBaseModel): + """ + an association which has a macromolecular machine mixin as a subject + """ + None + + + +class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineToEntityAssociationMixin, FunctionalAssociation): + """ + A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution. + """ + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToMolecularActivityAssociation","biolink:MacromolecularMachineToMolecularActivityAssociation"]] = Field(["biolink:MacromolecularMachineToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineToEntityAssociationMixin, FunctionalAssociation): + """ + A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it. + """ + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToBiologicalProcessAssociation","biolink:MacromolecularMachineToBiologicalProcessAssociation"]] = Field(["biolink:MacromolecularMachineToBiologicalProcessAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineToEntityAssociationMixin, FunctionalAssociation): + """ + A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component. + """ + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToCellularComponentAssociation","biolink:MacromolecularMachineToCellularComponentAssociation"]] = Field(["biolink:MacromolecularMachineToCellularComponentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MolecularActivityToChemicalEntityAssociation(Association): + """ + Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToChemicalEntityAssociation","biolink:MolecularActivityToChemicalEntityAssociation"]] = Field(["biolink:MolecularActivityToChemicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class MolecularActivityToMolecularActivityAssociation(Association): + """ + Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToMolecularActivityAssociation","biolink:MolecularActivityToMolecularActivityAssociation"]] = Field(["biolink:MolecularActivityToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneToGoTermAssociation(FunctionalAssociation): + + subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToGoTermAssociation","biolink:GeneToGoTermAssociation"]] = Field(["biolink:GeneToGoTermAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EntityToDiseaseAssociation(Association): + + FDA_approval_status: Optional[FDAApprovalStatusEnum] = Field(None) + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/EntityToDiseaseAssociation","biolink:EntityToDiseaseAssociation"]] = Field(["biolink:EntityToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class EntityToPhenotypicFeatureAssociation(Association): + + FDA_approval_status: Optional[FDAApprovalStatusEnum] = Field(None) + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociation","biolink:EntityToPhenotypicFeatureAssociation"]] = Field(["biolink:EntityToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SequenceAssociation(Association): + """ + An association between a sequence feature and a nucleic acid entity it is localized to. + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/SequenceAssociation","biolink:SequenceAssociation"]] = Field(["biolink:SequenceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GenomicSequenceLocalization(SequenceAssociation): + """ + A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig. + """ + start_interbase_coordinate: Optional[int] = Field(None, description="""The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).""") + end_interbase_coordinate: Optional[int] = Field(None, description="""The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.""") + genome_build: Optional[StrandEnum] = Field(None, description="""The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens.""") + strand: Optional[StrandEnum] = Field(None, description="""The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).""") + phase: Optional[PhaseEnum] = Field(None, description="""The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.""") + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GenomicSequenceLocalization","biolink:GenomicSequenceLocalization"]] = Field(["biolink:GenomicSequenceLocalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class SequenceFeatureRelationship(Association): + """ + For example, a particular exon is part of a particular transcript or gene + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/SequenceFeatureRelationship","biolink:SequenceFeatureRelationship"]] = Field(["biolink:SequenceFeatureRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class TranscriptToGeneRelationship(SequenceFeatureRelationship): + """ + A gene is a collection of transcripts + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/TranscriptToGeneRelationship","biolink:TranscriptToGeneRelationship"]] = Field(["biolink:TranscriptToGeneRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class GeneToGeneProductRelationship(SequenceFeatureRelationship): + """ + A gene is transcribed and potentially translated to a gene product + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneProductRelationship","biolink:GeneToGeneProductRelationship"]] = Field(["biolink:GeneToGeneProductRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ExonToTranscriptRelationship(SequenceFeatureRelationship): + """ + A transcript is formed from multiple exons + """ + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ExonToTranscriptRelationship","biolink:ExonToTranscriptRelationship"]] = Field(["biolink:ExonToTranscriptRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): + """ + A regulatory relationship between two genes + """ + object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""the direction is always from regulator to regulated""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation","biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"]] = Field(["biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class AnatomicalEntityToAnatomicalEntityAssociation(Association): + + subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityAssociation","biolink:AnatomicalEntityToAnatomicalEntityAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnatomicalEntityAssociation): + """ + A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms + """ + subject: str = Field(..., description="""the part""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the whole""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityPartOfAssociation","biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToAnatomicalEntityAssociation): + """ + A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship. + """ + subject: str = Field(..., description="""the structure at a later time""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the structure at an earlier time""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityOntogenicAssociation","biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class OrganismTaxonToEntityAssociation(ConfiguredBaseModel): + """ + An association between an organism taxon and another entity + """ + None + + + +class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, Association): + """ + A relationship between two organism taxon nodes + """ + subject: str = Field(..., description="""organism taxon that is the subject of the association""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation","biolink:OrganismTaxonToOrganismTaxonAssociation"]] = Field(["biolink:OrganismTaxonToOrganismTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAssociation): + """ + A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo + """ + subject: str = Field(..., description="""the more specific taxon""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the more general taxon""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonSpecialization","biolink:OrganismTaxonToOrganismTaxonSpecialization"]] = Field(["biolink:OrganismTaxonToOrganismTaxonSpecialization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssociation): + """ + An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens + """ + associated_environmental_context: Optional[str] = Field(None, description="""the environment in which the two taxa interact""") + subject: str = Field(..., description="""the taxon that is the subject of the association""") + predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") + object: str = Field(..., description="""the taxon that is the subject of the association""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonInteraction","biolink:OrganismTaxonToOrganismTaxonInteraction"]] = Field(["biolink:OrganismTaxonToOrganismTaxonInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, Association): + + subject: str = Field(..., description="""the taxon that is the subject of the association""") + predicate: str = Field(..., description="""predicate describing the relationship between the taxon and the environment""") + object: str = Field(..., description="""the environment in which the organism occurs""") + negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") + qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") + knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") + primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") + aggregator_knowledge_source: Optional[List[str]] = Field(None, description="""An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.""") + timepoint: Optional[str] = Field(None, description="""a point in time""") + original_subject: Optional[str] = Field(None, description="""used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_predicate: Optional[str] = Field(None, description="""used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.""") + original_object: Optional[str] = Field(None, description="""used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.""") + subject_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category: Optional[str] = Field(None, description="""Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_closure: Optional[List[str]] = Field(None, description="""Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_category_closure: Optional[List[str]] = Field(None, description="""Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_namespace: Optional[str] = Field(None, description="""Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_namespace: Optional[str] = Field(None, description="""Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + subject_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + object_label_closure: Optional[List[str]] = Field(None, description="""Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.""") + retrieval_source_ids: Optional[List[str]] = Field(None, description="""A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToEnvironmentAssociation","biolink:OrganismTaxonToEnvironmentAssociation"]] = Field(["biolink:OrganismTaxonToEnvironmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None) + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + + +class InformationResourceContainer(ConfiguredBaseModel): + """ + A collection of information resources + """ + information_resources: Optional[List[InformationResource]] = Field(default_factory=list, description="""a collection of information resources""") + + + +class InformationResource(ConfiguredBaseModel): + """ + A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb. + """ + status: Optional[InformationResourceStatusEnum] = Field(None, description="""the status of the infores identifier, the default is \"released\"""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + description: Optional[str] = Field(None) + + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +MappingCollection.update_forward_refs() +PredicateMapping.update_forward_refs() +OntologyClass.update_forward_refs() +Annotation.update_forward_refs() +QuantityValue.update_forward_refs() +RelationshipQuantifier.update_forward_refs() +SensitivityQuantifier.update_forward_refs() +SpecificityQuantifier.update_forward_refs() +PathognomonicityQuantifier.update_forward_refs() +FrequencyQuantifier.update_forward_refs() +ChemicalOrDrugOrTreatment.update_forward_refs() +Entity.update_forward_refs() +NamedThing.update_forward_refs() +Attribute.update_forward_refs() +ChemicalRole.update_forward_refs() +BiologicalSex.update_forward_refs() +PhenotypicSex.update_forward_refs() +GenotypicSex.update_forward_refs() +SeverityValue.update_forward_refs() +RelationshipType.update_forward_refs() +TaxonomicRank.update_forward_refs() +OrganismTaxon.update_forward_refs() +Event.update_forward_refs() +AdministrativeEntity.update_forward_refs() +Agent.update_forward_refs() +InformationContentEntity.update_forward_refs() +StudyResult.update_forward_refs() +StudyVariable.update_forward_refs() +CommonDataElement.update_forward_refs() +ConceptCountAnalysisResult.update_forward_refs() +ObservedExpectedFrequencyAnalysisResult.update_forward_refs() +RelativeFrequencyAnalysisResult.update_forward_refs() +TextMiningResult.update_forward_refs() +ChiSquaredAnalysisResult.update_forward_refs() +LogOddsAnalysisResult.update_forward_refs() +Dataset.update_forward_refs() +DatasetDistribution.update_forward_refs() +DatasetVersion.update_forward_refs() +DatasetSummary.update_forward_refs() +ConfidenceLevel.update_forward_refs() +EvidenceType.update_forward_refs() +Publication.update_forward_refs() +Book.update_forward_refs() +BookChapter.update_forward_refs() +Serial.update_forward_refs() +Article.update_forward_refs() +JournalArticle.update_forward_refs() +Patent.update_forward_refs() +WebPage.update_forward_refs() +PreprintPublication.update_forward_refs() +DrugLabel.update_forward_refs() +RetrievalSource.update_forward_refs() +PhysicalEssenceOrOccurrent.update_forward_refs() +PhysicalEssence.update_forward_refs() +PhysicalEntity.update_forward_refs() +Occurrent.update_forward_refs() +ActivityAndBehavior.update_forward_refs() +Activity.update_forward_refs() +Study.update_forward_refs() +Procedure.update_forward_refs() +Phenomenon.update_forward_refs() +Device.update_forward_refs() +DiagnosticAid.update_forward_refs() +SubjectOfInvestigation.update_forward_refs() +MaterialSample.update_forward_refs() +PlanetaryEntity.update_forward_refs() +EnvironmentalProcess.update_forward_refs() +EnvironmentalFeature.update_forward_refs() +GeographicLocation.update_forward_refs() +GeographicLocationAtTime.update_forward_refs() +ThingWithTaxon.update_forward_refs() +BiologicalEntity.update_forward_refs() +GenomicEntity.update_forward_refs() +EpigenomicEntity.update_forward_refs() +BiologicalProcessOrActivity.update_forward_refs() +MolecularActivity.update_forward_refs() +BiologicalProcess.update_forward_refs() +Pathway.update_forward_refs() +PhysiologicalProcess.update_forward_refs() +Behavior.update_forward_refs() +OrganismAttribute.update_forward_refs() +PhenotypicQuality.update_forward_refs() +GeneticInheritance.update_forward_refs() +OrganismalEntity.update_forward_refs() +Bacterium.update_forward_refs() +Virus.update_forward_refs() +CellularOrganism.update_forward_refs() +Mammal.update_forward_refs() +Human.update_forward_refs() +Plant.update_forward_refs() +Invertebrate.update_forward_refs() +Vertebrate.update_forward_refs() +Fungus.update_forward_refs() +LifeStage.update_forward_refs() +IndividualOrganism.update_forward_refs() +PopulationOfIndividualOrganisms.update_forward_refs() +StudyPopulation.update_forward_refs() +DiseaseOrPhenotypicFeature.update_forward_refs() +Disease.update_forward_refs() +PhenotypicFeature.update_forward_refs() +BehavioralFeature.update_forward_refs() +AnatomicalEntity.update_forward_refs() +CellularComponent.update_forward_refs() +Cell.update_forward_refs() +CellLine.update_forward_refs() +GrossAnatomicalStructure.update_forward_refs() +ChemicalEntityOrGeneOrGeneProduct.update_forward_refs() +RegulatoryRegion.update_forward_refs() +AccessibleDnaRegion.update_forward_refs() +TranscriptionFactorBindingSite.update_forward_refs() +ChemicalEntityOrProteinOrPolypeptide.update_forward_refs() +ChemicalEntity.update_forward_refs() +MolecularEntity.update_forward_refs() +SmallMolecule.update_forward_refs() +ChemicalMixture.update_forward_refs() +NucleicAcidEntity.update_forward_refs() +MolecularMixture.update_forward_refs() +ComplexMolecularMixture.update_forward_refs() +ProcessedMaterial.update_forward_refs() +Drug.update_forward_refs() +EnvironmentalFoodContaminant.update_forward_refs() +FoodAdditive.update_forward_refs() +Food.update_forward_refs() +MacromolecularMachineMixin.update_forward_refs() +GeneOrGeneProduct.update_forward_refs() +Gene.update_forward_refs() +GeneProductMixin.update_forward_refs() +GeneProductIsoformMixin.update_forward_refs() +MacromolecularComplex.update_forward_refs() +NucleosomeModification.update_forward_refs() +Genome.update_forward_refs() +Exon.update_forward_refs() +Transcript.update_forward_refs() +CodingSequence.update_forward_refs() +Polypeptide.update_forward_refs() +Protein.update_forward_refs() +ProteinIsoform.update_forward_refs() +PosttranslationalModification.update_forward_refs() +NucleicAcidSequenceMotif.update_forward_refs() +RNAProduct.update_forward_refs() +RNAProductIsoform.update_forward_refs() +NoncodingRNAProduct.update_forward_refs() +MicroRNA.update_forward_refs() +SiRNA.update_forward_refs() +GeneGroupingMixin.update_forward_refs() +ProteinDomain.update_forward_refs() +ProteinFamily.update_forward_refs() +GeneFamily.update_forward_refs() +Zygosity.update_forward_refs() +Genotype.update_forward_refs() +Haplotype.update_forward_refs() +SequenceVariant.update_forward_refs() +Snv.update_forward_refs() +ReagentTargetedGene.update_forward_refs() +ClinicalAttribute.update_forward_refs() +ClinicalMeasurement.update_forward_refs() +ClinicalModifier.update_forward_refs() +ClinicalCourse.update_forward_refs() +Onset.update_forward_refs() +ClinicalEntity.update_forward_refs() +ClinicalTrial.update_forward_refs() +ClinicalIntervention.update_forward_refs() +ClinicalFinding.update_forward_refs() +Hospitalization.update_forward_refs() +SocioeconomicAttribute.update_forward_refs() +Case.update_forward_refs() +Cohort.update_forward_refs() +ExposureEvent.update_forward_refs() +GenomicBackgroundExposure.update_forward_refs() +PathologicalEntityMixin.update_forward_refs() +PathologicalProcess.update_forward_refs() +PathologicalProcessExposure.update_forward_refs() +PathologicalAnatomicalStructure.update_forward_refs() +PathologicalAnatomicalExposure.update_forward_refs() +DiseaseOrPhenotypicFeatureExposure.update_forward_refs() +ChemicalExposure.update_forward_refs() +ComplexChemicalExposure.update_forward_refs() +DrugExposure.update_forward_refs() +DrugToGeneInteractionExposure.update_forward_refs() +Treatment.update_forward_refs() +BioticExposure.update_forward_refs() +EnvironmentalExposure.update_forward_refs() +GeographicExposure.update_forward_refs() +BehavioralExposure.update_forward_refs() +SocioeconomicExposure.update_forward_refs() +Outcome.update_forward_refs() +PathologicalProcessOutcome.update_forward_refs() +PathologicalAnatomicalOutcome.update_forward_refs() +DiseaseOrPhenotypicFeatureOutcome.update_forward_refs() +BehavioralOutcome.update_forward_refs() +HospitalizationOutcome.update_forward_refs() +MortalityOutcome.update_forward_refs() +EpidemiologicalOutcome.update_forward_refs() +SocioeconomicOutcome.update_forward_refs() +Association.update_forward_refs() +ChemicalEntityAssessesNamedThingAssociation.update_forward_refs() +ContributorAssociation.update_forward_refs() +GenotypeToGenotypePartAssociation.update_forward_refs() +GenotypeToGeneAssociation.update_forward_refs() +GenotypeToVariantAssociation.update_forward_refs() +GeneToGeneAssociation.update_forward_refs() +GeneToGeneHomologyAssociation.update_forward_refs() +GeneToGeneFamilyAssociation.update_forward_refs() +GeneExpressionMixin.update_forward_refs() +GeneToGeneCoexpressionAssociation.update_forward_refs() +PairwiseGeneToGeneInteraction.update_forward_refs() +PairwiseMolecularInteraction.update_forward_refs() +CellLineToEntityAssociationMixin.update_forward_refs() +ChemicalEntityToEntityAssociationMixin.update_forward_refs() +DrugToEntityAssociationMixin.update_forward_refs() +ChemicalToEntityAssociationMixin.update_forward_refs() +CaseToEntityAssociationMixin.update_forward_refs() +ChemicalToChemicalAssociation.update_forward_refs() +ReactionToParticipantAssociation.update_forward_refs() +ReactionToCatalystAssociation.update_forward_refs() +ChemicalToChemicalDerivationAssociation.update_forward_refs() +MolecularActivityToPathwayAssociation.update_forward_refs() +ChemicalToPathwayAssociation.update_forward_refs() +NamedThingAssociatedWithLikelihoodOfNamedThingAssociation.update_forward_refs() +ChemicalGeneInteractionAssociation.update_forward_refs() +ChemicalAffectsGeneAssociation.update_forward_refs() +DrugToGeneAssociation.update_forward_refs() +MaterialSampleToEntityAssociationMixin.update_forward_refs() +MaterialSampleDerivationAssociation.update_forward_refs() +DiseaseToEntityAssociationMixin.update_forward_refs() +EntityToExposureEventAssociationMixin.update_forward_refs() +DiseaseToExposureEventAssociation.update_forward_refs() +EntityToOutcomeAssociationMixin.update_forward_refs() +ExposureEventToOutcomeAssociation.update_forward_refs() +FrequencyQualifierMixin.update_forward_refs() +EntityToFeatureOrDiseaseQualifiersMixin.update_forward_refs() +EntityToPhenotypicFeatureAssociationMixin.update_forward_refs() +InformationContentEntityToNamedThingAssociation.update_forward_refs() +EntityToDiseaseAssociationMixin.update_forward_refs() +DiseaseOrPhenotypicFeatureToEntityAssociationMixin.update_forward_refs() +DiseaseOrPhenotypicFeatureToLocationAssociation.update_forward_refs() +DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation.update_forward_refs() +EntityToDiseaseOrPhenotypicFeatureAssociationMixin.update_forward_refs() +CellLineToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() +ChemicalToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() +ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() +ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() +MaterialSampleToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() +GenotypeToEntityAssociationMixin.update_forward_refs() +GenotypeToPhenotypicFeatureAssociation.update_forward_refs() +ExposureEventToPhenotypicFeatureAssociation.update_forward_refs() +DiseaseToPhenotypicFeatureAssociation.update_forward_refs() +CaseToPhenotypicFeatureAssociation.update_forward_refs() +BehaviorToBehavioralFeatureAssociation.update_forward_refs() +GeneToEntityAssociationMixin.update_forward_refs() +GeneToPathwayAssociation.update_forward_refs() +VariantToEntityAssociationMixin.update_forward_refs() +GeneToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() +GeneToPhenotypeAssociation.update_forward_refs() +GeneToDiseaseAssociation.update_forward_refs() +CausalGeneToDiseaseAssociation.update_forward_refs() +CorrelatedGeneToDiseaseAssociation.update_forward_refs() +DruggableGeneToDiseaseAssociation.update_forward_refs() +VariantToGeneAssociation.update_forward_refs() +VariantToGeneExpressionAssociation.update_forward_refs() +VariantToPopulationAssociation.update_forward_refs() +PopulationToPopulationAssociation.update_forward_refs() +VariantToPhenotypicFeatureAssociation.update_forward_refs() +VariantToDiseaseAssociation.update_forward_refs() +GenotypeToDiseaseAssociation.update_forward_refs() +ModelToDiseaseAssociationMixin.update_forward_refs() +GeneAsAModelOfDiseaseAssociation.update_forward_refs() +VariantAsAModelOfDiseaseAssociation.update_forward_refs() +GenotypeAsAModelOfDiseaseAssociation.update_forward_refs() +CellLineAsAModelOfDiseaseAssociation.update_forward_refs() +OrganismalEntityAsAModelOfDiseaseAssociation.update_forward_refs() +OrganismToOrganismAssociation.update_forward_refs() +TaxonToTaxonAssociation.update_forward_refs() +GeneHasVariantThatContributesToDiseaseAssociation.update_forward_refs() +GeneToExpressionSiteAssociation.update_forward_refs() +SequenceVariantModulatesTreatmentAssociation.update_forward_refs() +FunctionalAssociation.update_forward_refs() +MacromolecularMachineToEntityAssociationMixin.update_forward_refs() +MacromolecularMachineToMolecularActivityAssociation.update_forward_refs() +MacromolecularMachineToBiologicalProcessAssociation.update_forward_refs() +MacromolecularMachineToCellularComponentAssociation.update_forward_refs() +MolecularActivityToChemicalEntityAssociation.update_forward_refs() +MolecularActivityToMolecularActivityAssociation.update_forward_refs() +GeneToGoTermAssociation.update_forward_refs() +EntityToDiseaseAssociation.update_forward_refs() +EntityToPhenotypicFeatureAssociation.update_forward_refs() +SequenceAssociation.update_forward_refs() +GenomicSequenceLocalization.update_forward_refs() +SequenceFeatureRelationship.update_forward_refs() +TranscriptToGeneRelationship.update_forward_refs() +GeneToGeneProductRelationship.update_forward_refs() +ExonToTranscriptRelationship.update_forward_refs() +ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation.update_forward_refs() +AnatomicalEntityToAnatomicalEntityAssociation.update_forward_refs() +AnatomicalEntityToAnatomicalEntityPartOfAssociation.update_forward_refs() +AnatomicalEntityToAnatomicalEntityOntogenicAssociation.update_forward_refs() +OrganismTaxonToEntityAssociation.update_forward_refs() +OrganismTaxonToOrganismTaxonAssociation.update_forward_refs() +OrganismTaxonToOrganismTaxonSpecialization.update_forward_refs() +OrganismTaxonToOrganismTaxonInteraction.update_forward_refs() +OrganismTaxonToEnvironmentAssociation.update_forward_refs() +InformationResourceContainer.update_forward_refs() +InformationResource.update_forward_refs() + diff --git a/context.jsonld b/context.jsonld index d85bc98cc2..f2c87bdf50 100644 --- a/context.jsonld +++ b/context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-05-23T23:04:19", + "generation_date": "2023-05-23T23:22:44", "source": "biolink-model.yaml" }, "@context": { diff --git a/contextn.jsonld b/contextn.jsonld index 36def9d573..e4a8af0d77 100644 --- a/contextn.jsonld +++ b/contextn.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-05-23T23:04:25", + "generation_date": "2023-05-23T23:22:49", "source": "biolink-model.yaml" }, "@context": {