From 0b6767355e480885beff565ab455e1a5aaa5f705 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 30 Jun 2023 21:22:12 +0000 Subject: [PATCH] Regenerate artifacts from biolink-model.yaml --- biolink-model.owl.ttl | 1206 +- biolink-model.shacl.ttl | 28900 +++++++++++++++++++------------------- biolink-model.ttl | 572 +- biolink/model.py | 2 +- context.jsonld | 2 +- contextn.jsonld | 2 +- 6 files changed, 15342 insertions(+), 15342 deletions(-) diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index 3acd1badbb..0828dd50c6 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -155,13 +155,13 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty rdf:subject ; @@ -183,6 +183,18 @@ 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 biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], + [ 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 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty biolink:has_quotient ], @@ -190,10 +202,6 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:onClass biolink:BehavioralFeature ; owl:onProperty rdf:object ; @@ -204,24 +212,16 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_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 ], 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." ; @@ -282,24 +282,12 @@ 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 ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ 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 ], - [ 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:BiologicalSex ; @@ -312,6 +300,18 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; 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:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_total ], biolink:Association, biolink:CaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -354,21 +354,21 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:CellLine ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:CellLine ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin ; @@ -380,29 +380,21 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onClass biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onClass biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DirectionQualifierEnum ; @@ -412,45 +404,53 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; owl:onClass biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + 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 ; owl:qualifiedCardinality 1 ], [ 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:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ 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_aspect_qualifier ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:qualified_predicate ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:qualified_predicate ], 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 "{}" ; @@ -459,6 +459,10 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -466,10 +470,6 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:Association ; linkml:attributes "{}" ; linkml:is_a "association" . @@ -484,14 +484,14 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], biolink:Association ; skos:definition "A regulatory relationship between two genes" ; linkml:attributes "{}" ; @@ -500,49 +500,49 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:AnatomicalEntity ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + 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:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:ChemicalEntity ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], [ 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:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:object_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)" ; @@ -573,11 +573,11 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; @@ -710,20 +710,20 @@ biolink:ConceptCountAnalysisResult a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:InformationContentEntity ; + 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:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:onClass biolink:Agent ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:InformationContentEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; linkml:attributes "{}" ; @@ -772,13 +772,13 @@ biolink:DiseaseOrPhenotypicFeatureOutcome a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneticInheritance ; - 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:GeneticInheritance ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; @@ -813,25 +813,37 @@ 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:Disease ; - 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 linkml:Double ; owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; - owl:onClass biolink:PhenotypicFeature ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:onClass biolink:Disease ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; @@ -840,18 +852,6 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; 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 linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:DiseaseToEntityAssociationMixin, biolink:EntityToPhenotypicFeatureAssociationMixin ; @@ -899,16 +899,16 @@ 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: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:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], biolink:EntityToDiseaseAssociationMixin, biolink:GeneToDiseaseAssociation, biolink:GeneToEntityAssociationMixin ; @@ -980,13 +980,13 @@ 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 "{}" ; @@ -1013,40 +1013,40 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + 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: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 linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:BiologicalSex ; owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + 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:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ 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 linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:has_count ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; @@ -1098,21 +1098,21 @@ biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass 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:onClass biolink:Disease ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass 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" . @@ -1120,25 +1120,25 @@ 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:AnatomicalEntity ; - owl:onProperty rdf:object ; + 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:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; linkml:attributes "{}" ; @@ -1147,10 +1147,6 @@ 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 ], @@ -1158,14 +1154,18 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], biolink:GeneExpressionMixin, biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; @@ -1176,6 +1176,10 @@ 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:GeneFamily ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -1183,10 +1187,6 @@ biolink:GeneToGeneFamilyAssociation 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: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 "{}" ; @@ -1198,14 +1198,14 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], 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 "{}" ; @@ -1214,13 +1214,13 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:GeneProductMixin ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:GeneProductMixin ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; @@ -1233,13 +1233,13 @@ biolink:GeneToGeneProductRelationship a owl:Class ; biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:OntologyClass ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:OntologyClass ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; skos:exactMatch WBVocab:Gene-GO-Association ; @@ -1306,19 +1306,19 @@ biolink:Genome a owl:Class ; biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:TimeType ; owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; @@ -1357,16 +1357,16 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:Gene ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:Genotype ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; @@ -1395,33 +1395,21 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:onClass biolink:Genotype ; owl:onProperty rdf:subject ; @@ -1430,10 +1418,22 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; 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:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ 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:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; @@ -1446,6 +1446,10 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:Genotype ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], @@ -1453,10 +1457,6 @@ biolink:GenotypeToVariantAssociation a owl:Class ; 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 ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." ; linkml:attributes "{}" ; @@ -1705,13 +1705,13 @@ biolink:MicroRNA a owl:Class ; biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:ChemicalEntity ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:MolecularActivity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; linkml:attributes "{}" ; @@ -1721,11 +1721,11 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:MolecularActivity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; @@ -1735,16 +1735,16 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + 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:Pathway ; - owl:onProperty rdf:object ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; @@ -1766,20 +1766,20 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_context_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:subject_context_qualifier ], + owl:onClass linkml:String ; + owl:onProperty biolink:object_aspect_qualifier ], biolink:Association ; skos:definition "" ; linkml:attributes "{}" ; @@ -1796,12 +1796,12 @@ 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, @@ -1843,21 +1843,21 @@ 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: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:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], 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 "{}" ; @@ -1899,21 +1899,21 @@ 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 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:onClass biolink:OrganismalEntity ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:ModelToDiseaseAssociationMixin ; @@ -1925,13 +1925,9 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:onClass biolink:MolecularEntity ; owl:onProperty rdf:object ; @@ -1941,9 +1937,13 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:interacting_molecules_category ], + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; linkml:attributes "{}" ; @@ -2099,16 +2099,16 @@ biolink:Plant a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; + owl: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:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:subject ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a two populations" ; @@ -2261,13 +2261,13 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:SequenceVariant ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:Treatment ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; linkml:attributes "{}" ; @@ -2276,9 +2276,9 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty rdf:type ], @@ -2287,9 +2287,9 @@ biolink:Serial a owl:Class ; owl:onClass linkml:String ; owl:onProperty biolink:volume ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -2351,16 +2351,16 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], - [ a owl:Class ; + rdfs:subClassOf [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ] [ a owl:Restriction ; owl:onProperty biolink:has_attribute ; owl:someValuesFrom biolink:SocioeconomicAttribute ] ) ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], biolink:Attribute, biolink:ExposureEvent ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; @@ -2467,13 +2467,13 @@ 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:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:DiseaseOrPhenotypicFeature ; @@ -2497,24 +2497,32 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ 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 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; owl:onClass biolink:SequenceVariant ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; @@ -2523,14 +2531,6 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:FrequencyValue ; owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:VariantToEntityAssociationMixin ; @@ -2542,33 +2542,33 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ 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: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:PopulationOfIndividualOrganisms ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], [ 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 linkml:Integer ; + 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 linkml:Integer ; - owl:onProperty biolink:has_total ], + owl:onClass biolink:SequenceVariant ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association, biolink:FrequencyQualifierMixin, biolink:FrequencyQuantifier, @@ -3466,7 +3466,7 @@ biolink:Article a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -3478,7 +3478,7 @@ biolink:Article a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], 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, @@ -3512,13 +3512,13 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:volume ], - [ 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:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -3774,29 +3774,29 @@ biolink:GeneOrGeneProductOrChemicalEntityAspectEnum a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to 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 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:onClass biolink:NamedThing ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, biolink:GenotypeToEntityAssociationMixin ; @@ -3810,11 +3810,11 @@ biolink:GeographicLocation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty biolink:latitude ], + owl:onProperty biolink:longitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, @@ -3895,10 +3895,6 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:MolecularEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ReactionDirectionEnum ; owl:onProperty biolink:reaction_direction ], @@ -3906,6 +3902,10 @@ biolink:ReactionToParticipantAssociation a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:stoichiometry ], + [ a owl:Restriction ; + owl:onClass biolink:MolecularEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ReactionSideEnum ; @@ -3937,24 +3937,24 @@ biolink:StudyPopulation a owl:Class ; linkml:is_a "population of individual organisms" . biolink:SymbolType a owl:Class ; - rdfs:label "symbol type" ; - rdfs:subClassOf linkml:String . - -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:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; + rdfs:label "symbol type" ; + rdfs:subClassOf linkml:String . + +biolink:Treatment a owl:Class ; + rdfs:label "treatment" ; + rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:Procedure ; owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Device ; + owl:onProperty biolink:has_device ], biolink:ChemicalOrDrugOrTreatment, biolink:ExposureEvent, biolink:NamedThing ; @@ -3972,28 +3972,28 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:FrequencyValue ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl: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 biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:SeverityValue ; owl:onProperty biolink:severity_qualifier ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], [ 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:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:EntityToDiseaseAssociationMixin, @@ -6393,11 +6393,11 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:AnatomicalEntity ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; linkml:attributes "{}" ; @@ -6779,8 +6779,8 @@ 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 ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; @@ -6791,8 +6791,8 @@ biolink:FrequencyQuantifier a owl:Class ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], biolink:RelationshipQuantifier, linkml:mixin ; linkml:attributes "{}" ; @@ -7005,9 +7005,13 @@ biolink:FrequencyQuantifier a owl:Class ; biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:onClass linkml:Double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:onClass biolink:PredicateType ; owl:onProperty rdf:predicate ; @@ -7018,23 +7022,15 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:SeverityValue ; - owl:onProperty biolink:severity_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty rdf:object ; + owl:onClass biolink:GeneOrGeneProduct ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; @@ -7042,20 +7038,24 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onClass biolink:SeverityValue ; + owl:onProperty biolink:severity_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + 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 ], + owl:onClass biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], + owl:onClass biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:FrequencyValue ; + owl:onProperty biolink:frequency_qualifier ], biolink:Association, biolink:EntityToPhenotypicFeatureAssociationMixin, biolink:GeneToEntityAssociationMixin ; @@ -7115,11 +7115,11 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:OrganismTaxon ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association, biolink:OrganismTaxonToEntityAssociation ; @@ -7959,20 +7959,20 @@ biolink:GeneExpressionMixin a owl:Class ; rdfs:label "gene expression mixin" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + 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:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:onClass biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], linkml:mixin ; skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; linkml:attributes "{}" . @@ -7981,11 +7981,11 @@ biolink:GeneToGeneAssociation a owl:Class ; rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:object ; + owl:onProperty rdf:subject ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass biolink:GeneOrGeneProduct ; - owl:onProperty rdf:subject ; + owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], biolink:Association ; skos:altLabel "molecular or genetic interaction" ; @@ -8062,10 +8062,7 @@ biolink:PredicateMapping a owl:Class ; rdfs:subClassOf [ 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:narrow_match ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -8073,73 +8070,76 @@ biolink:PredicateMapping a owl:Class ; [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_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:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onClass linkml:String ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onClass linkml:String ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:onClass linkml:String ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:object_part_qualifier ], + owl:onClass biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + 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:object_context_qualifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_derivative_qualifier ], + 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:mapped_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:mapped_predicate ] ; + owl:onClass biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ] ; 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 "{}" . @@ -8415,16 +8415,16 @@ biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:ingest_date ], + owl:onClass biolink:DatasetDistribution ; + owl:onProperty dct:distribution ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Dataset ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:DatasetDistribution ; - owl:onProperty dct:distribution ], + owl:onClass linkml:String ; + owl:onProperty biolink:ingest_date ], biolink:InformationContentEntity ; skos:definition "an item that holds version level information about a dataset." ; linkml:attributes "{}" ; @@ -8433,13 +8433,13 @@ biolink:DatasetVersion a owl:Class ; biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:MacromolecularMachineMixin ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass biolink:OntologyClass ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass biolink:MacromolecularMachineMixin ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], biolink:Association ; skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; linkml:attributes "{}" ; @@ -8863,14 +8863,14 @@ biolink:LifeStage a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:enabled_by ], biolink:BiologicalProcessOrActivity, biolink:Occurrent, biolink:OntologyClass ; @@ -8892,14 +8892,14 @@ biolink:RetrievalSource a owl:Class ; owl:onClass biolink:ResourceRoleEnum ; owl:onProperty biolink:resource_role ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:resource_id ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Uriorcurie ; owl:onProperty biolink:upstream_resource_ids ], + [ a owl:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:resource_id ; + owl:qualifiedCardinality 1 ], biolink:InformationContentEntity ; skos:definition "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." ; linkml:attributes "{}" ; @@ -9054,6 +9054,10 @@ biolink:ChemicalMixture a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:ChemicalMixture ; owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -9061,10 +9065,6 @@ biolink:ChemicalMixture a owl:Class ; [ 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 ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -9168,12 +9168,12 @@ biolink:StudyResult a owl:Class ; biolink:ThingWithTaxon a owl:Class ; rdfs:label "thing with taxon" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], linkml:mixin ; skos:definition "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" ; linkml:attributes "{}" . @@ -9430,16 +9430,20 @@ biolink:supporting_study_metadata a owl:ObjectProperty ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:NarrativeText ; + owl:onProperty dct:description ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty rdf:type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:IriType ; - owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:allValuesFrom biolink:Attribute ; owl:onProperty biolink:has_attribute ], @@ -9448,25 +9452,21 @@ biolink:Entity a owl:Class ; owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:NarrativeText ; - owl:onProperty dct:description ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ] ; + owl:onClass biolink:IriType ; + owl:onProperty biolink:iri ] ; 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:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:Zygosity ; owl:onProperty biolink:has_zygosity ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -9615,24 +9615,24 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ; rdfs:label "entity to phenotypic feature association mixin" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty biolink:has_quotient ], - [ 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 ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:has_count ], + owl:onClass biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ 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_quotient ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; @@ -9767,13 +9767,13 @@ biolink:Drug a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass biolink:NucleicAcidEntity ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:StrandEnum ; + owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:onClass biolink:PredicateType ; - owl:onProperty rdf:predicate ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:StrandEnum ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:PhaseEnum ; @@ -9783,21 +9783,21 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:onProperty rdf:object ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty biolink:end_interbase_coordinate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:StrandEnum ; - owl:onProperty biolink:strand ], + owl:onClass biolink:NucleicAcidEntity ; + owl:onProperty rdf:subject ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:StrandEnum ; - owl:onProperty biolink:genome_build ], + owl:onClass linkml:Integer ; + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:end_interbase_coordinate ], + [ a owl:Restriction ; + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -9948,16 +9948,16 @@ biolink:EntityToDiseaseAssociationMixin a owl:Class ; biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], biolink:GenomicEntity, biolink:MolecularEntity, biolink:OntologyClass, @@ -10042,20 +10042,20 @@ biolink:timepoint a owl:ObjectProperty ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ 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 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:address ], + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -10171,21 +10171,21 @@ biolink:Occurrent a owl:Class ; biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:license ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Date ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:rights ], + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:format ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:rights ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -10231,6 +10231,13 @@ biolink:LabelType a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:NamedThing ; + owl:onProperty biolink:has_qualitative_value ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:LabelType ; owl:onProperty rdfs:label ], @@ -10238,13 +10245,6 @@ biolink:Attribute a owl:Class ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ; owl:qualifiedCardinality 1 ], - [ 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 ], 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." ; @@ -10304,16 +10304,16 @@ biolink:AnatomicalEntity a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:BiologicalSequence ; - owl:onProperty biolink:has_biological_sequence ], + owl:onClass linkml:String ; + owl:onProperty biolink:id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene ], [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty biolink:id ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:BiologicalSequence ; + owl:onProperty biolink:has_biological_sequence ], biolink:BiologicalEntity, biolink:GenomicEntity, biolink:OntologyClass, @@ -10337,6 +10337,10 @@ biolink:Publication a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:pages ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty rdfs:label ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:keywords ], @@ -10344,16 +10348,6 @@ biolink:Publication a owl:Class ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:summary ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty rdfs:label ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:authors ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:mesh_terms ], [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom linkml:String ; @@ -10364,6 +10358,12 @@ biolink:Publication a owl:Class ; owl:onClass linkml:String ; owl:onProperty biolink:id ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:mesh_terms ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:authors ], biolink:InformationContentEntity ; skos:definition "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). " ; skos:exactMatch IAO:0000311 ; @@ -10376,22 +10376,22 @@ biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ 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 ], + owl:onClass biolink:ChemicalEntity ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:allValuesFrom biolink:DrugAvailabilityEnum ; owl:onProperty biolink:available_from ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:ChemicalEntity ; - owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; 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 ], biolink:ChemicalEntityOrGeneOrGeneProduct, biolink:ChemicalEntityOrProteinOrPolypeptide, biolink:ChemicalOrDrugOrTreatment, @@ -10413,12 +10413,12 @@ biolink:ChemicalEntity a owl:Class ; biolink:Gene a owl:Class ; rdfs:label "gene" ; 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 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -10559,100 +10559,100 @@ 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 ], + owl:allValuesFrom linkml:String ; + owl:onProperty rdf:type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty biolink:primary_knowledge_source ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], + owl:onProperty biolink:subject_namespace ], [ 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:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:TimeType ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass biolink:OntologyClass ; owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:subject_namespace ], + owl:allValuesFrom biolink:CategoryType ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:OntologyClass ; - owl:onProperty biolink:object_category ], + owl:onClass linkml:Boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:knowledge_source ], + owl:onClass linkml:Uriorcurie ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:subject ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:subject_label_closure ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty biolink:object_closure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category_closure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty biolink:negated ], + owl:onClass linkml:String ; + owl:onProperty biolink:object_namespace ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty biolink:object_closure ], + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty biolink:object_namespace ], + owl:onClass biolink:TimeType ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty biolink:object_label_closure ], + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:onClass biolink:NamedThing ; - owl:onProperty rdf:object ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty biolink:original_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], + owl:onClass linkml:String ; + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty biolink:subject_closure ], + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdf:type ], + owl:onClass biolink:PredicateType ; + owl:onProperty rdf:predicate ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:OntologyClass ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty biolink:knowledge_source ], + [ a owl:Restriction ; + owl:onClass biolink:NamedThing ; + owl:onProperty rdf:object ; + owl:qualifiedCardinality 1 ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -10663,22 +10663,22 @@ biolink:Association a owl:Class ; biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass biolink:LabelType ; - owl:onProperty biolink:full_name ], - [ a owl:Class ; + rdfs:subClassOf [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom biolink:CategoryType ; owl:onProperty biolink:category ] [ a owl:Restriction ; owl:onProperty biolink:category ; owl:someValuesFrom biolink:CategoryType ] ) ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty biolink:provided_by ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass biolink:LabelType ; + owl:onProperty biolink:full_name ], 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 3f4b5ad579..b299c66f6f 100644 --- a/biolink-model.shacl.ttl +++ b/biolink-model.shacl.ttl @@ -12,53 +12,39 @@ 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:description "The human readable scientific name for the taxon of the entity." ; 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 5 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path dct: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: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 1 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_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:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:order 9 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + 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 "connects a genomic feature to its sequence" ; - 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. @@ -67,24 +53,28 @@ 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: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 "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + 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:order 6 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct: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. + 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`, ... @@ -93,30 +83,40 @@ 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: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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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: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 "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:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path dct:description ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ 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 0 ; - sh:path biolink:provided_by ] ; + 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:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; @@ -128,33 +128,10 @@ biolink:ActivityAndBehavior a sh:NodeShape ; biolink:AdministrativeEntity a sh:NodeShape ; sh:closed false ; 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: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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_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 1 ; - sh:path biolink:xref ], - [ sh:order 6 ; - sh:path rdf:type ], - [ 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 7 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; @@ -164,63 +141,46 @@ 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:full_name ], + [ 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 0 ; - 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 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:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed false ; 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: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:RetrievalSource ; + 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 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: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: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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -228,56 +188,87 @@ 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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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 "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 "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 25 ; - sh:path biolink:id ], + 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: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: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 "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 "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 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 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: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 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 3 ; - 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:order 13 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 20 ; - 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 23 ; - sh:path biolink:object_label_closure ], + sh:order 10 ; + sh:path biolink:timepoint ], + [ 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: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 "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 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 15 ; + sh:path biolink:object_category ], + [ 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 ; + 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 12 ; @@ -287,261 +278,235 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t 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: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 "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: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 "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:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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 26 ; - sh:path biolink:iri ], - [ 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: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 "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: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 0 ; - sh:path rdf:subject ] ; + 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: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:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; - sh:maxCount 1 ; - sh:minCount 1 ; + 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 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: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 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 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: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: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 "a human-readable description of an entity" ; + 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:order 30 ; - sh:path dct:description ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; + 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 "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 "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:nodeKind sh:IRI ; - 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: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: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:AnatomicalEntity ; + sh:description "the structure at an earlier time" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + 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 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:description "Used to hold the 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: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 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: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 19 ; - sh:path biolink:object_category_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 "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ 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 point in time" ; 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: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: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: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 "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 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:class biolink:AnatomicalEntity ; + sh:description "the structure at a later time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 original relation/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 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:order 7 ; + 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 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: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 21 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the 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: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: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: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:timepoint ] ; + sh:order 13 ; + sh:path biolink:original_object ] ; 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: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 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 "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 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 "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 "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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:class biolink:AnatomicalEntity ; + sh:description "the whole" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + 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 "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: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 "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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:AnatomicalEntity ; sh:description "the part" ; sh:maxCount 1 ; @@ -549,77 +514,112 @@ 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 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 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: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: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 "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:class biolink:AnatomicalEntity ; - sh:description "the whole" ; - sh:maxCount 1 ; - sh:minCount 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 2 ; - sh:path rdf:object ], + 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: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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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: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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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 7 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + 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: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 30 ; - sh:path dct:description ], + 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 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: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 15 ; - sh:path biolink:object_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: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:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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: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 "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: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:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . biolink:Annotation a sh:NodeShape ; @@ -633,152 +633,124 @@ biolink:Article a sh:NodeShape ; 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 18 ; - 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 9 ; - sh:path biolink:xref ], - [ 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 "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 long-form human readable name for a thing" ; + sh:order 10 ; + sh:path biolink:license ], + [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:full_name ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:order 6 ; + sh:path biolink:summary ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:order 21 ; + sh:path dct: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: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 "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:iri ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + sh:path biolink:mesh_terms ], + [ sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:rights ], [ sh:maxCount 1 ; sh:order 12 ; sh:path biolink:format ], + [ 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 2 ; + sh:path biolink:volume ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:full_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 14 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + 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 13 ; sh:path biolink:creation_date ], - [ 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 16 ; - sh:path biolink:id ], + sh:order 18 ; + 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 9 ; + 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 5 ; sh:path biolink:pages ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_attribute ], - [ sh:description "executive summary of a publication" ; + [ 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 6 ; - sh:path biolink:summary ], + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:id ], [ sh:order 19 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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 17 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], - [ 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 "keywords tagging a publication" ; - sh:order 7 ; - sh:path biolink:keywords ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ 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 20 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ 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: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 "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: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: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: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 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: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: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: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: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 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: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 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: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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -789,75 +761,82 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ 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: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 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 "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 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: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: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: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 "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 point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ 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 "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; 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: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 30 ; + sh:path dct: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: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 "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 description of an entity" ; + [ 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 30 ; - sh:path dct:description ], + 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: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 ; @@ -865,24 +844,50 @@ 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 "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:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:qualifiers ] ; + 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: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 "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: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:description "a human-readable description of an entity" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + 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 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. @@ -892,118 +897,123 @@ 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:order 8 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct: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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "may often be an organism 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 2 ; - sh:path biolink:provided_by ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ 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 human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; 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 8 ; - 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 "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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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: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 "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 "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:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "total number of things in a particular reference set" ; 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:order 34 ; + 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:has_evidence ], + sh:order 5 ; + 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + 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 37 ; + 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 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: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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + [ 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:BehavioralFeature ; + sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; sh:minCount 1 ; 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: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 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 3 ; + 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:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], - [ sh:maxCount 1 ; - sh:order 35 ; - 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:order 38 ; + sh:path biolink:onset_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: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 37 ; - sh:path biolink:severity_qualifier ], - [ sh:description "a point in time" ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ 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 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: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 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:order 14 ; + 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 24 ; + 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 13 ; - sh:path biolink:original_predicate ], + 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:maxCount 1 ; sh:minCount 1 ; @@ -1013,182 +1023,172 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; 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 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 ; - 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], - [ sh:class biolink:BehavioralFeature ; - sh:description "behavioral feature that is the object of the association" ; + sh:order 31 ; + sh:path dct:description ], + [ 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 3 ; - 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 20 ; - sh:path biolink:object_category_closure ], + 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 "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 qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 39 ; + sh:path biolink:frequency_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 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: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: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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 21 ; + 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: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:nodeKind sh:IRI ; + sh:order 16 ; + 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:order 8 ; - sh:path biolink: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 6 ; - sh:path biolink:publications ], - [ 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 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: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 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "total number of things in a particular reference set" ; + sh:order 32 ; + 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 34 ; - 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:order 22 ; + 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:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_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: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 13 ; + sh:path biolink:original_predicate ], [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:order 36 ; 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 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 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 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 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:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ] ; 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 10 ; - 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:order 11 ; - sh:path rdf:type ], - [ 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: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 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: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 2 ; 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 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:full_name ], + [ 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 11 ; + sh:path rdf:type ], + [ 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 10 ; + 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:nodeKind sh:IRI ; sh:order 4 ; 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 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ 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: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:targetClass biolink:BehavioralExposure . biolink:BehavioralOutcome a sh:NodeShape ; @@ -1200,27 +1200,14 @@ biolink:BehavioralOutcome a sh:NodeShape ; biolink:BiologicalEntity a sh:NodeShape ; sh:closed false ; 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 ; - sh:path biolink:has_attribute ], - [ 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 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 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct: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:order 1 ; + 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. @@ -1230,97 +1217,110 @@ 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 "A unique identifier 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:order 8 ; + 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 6 ; sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path dct: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 3 ; + sh:path biolink:xref ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_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 3 ; - sh:path biolink:xref ], - [ sh:order 8 ; - 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 "A unique identifier 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: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: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 human-readable name for an attribute or entity." ; + sh:property [ 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 12 ; - 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 "The value in this node property represents the knowledge provider that created or assembled the node 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. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 10 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct: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: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 human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path rdfs:label ], [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + 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_output ], + sh:order 0 ; + 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 7 ; + sh:path biolink:xref ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path rdfs:label ], + [ sh:order 11 ; + 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 2 ; sh:path biolink:enabled_by ], - [ 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:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_input ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:order 11 ; - 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 1 ; + sh:path biolink:has_output ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 3 ; - sh:path biolink:id ], + sh:order 10 ; + 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:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + 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 9 ; @@ -1331,39 +1331,63 @@ 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: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 1 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], [ 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:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + 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 10 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:order 11 ; sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ 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:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; 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 4 ; + 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 5 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_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 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:path biolink:xref ], @@ -1371,47 +1395,14 @@ biolink:BioticExposure a sh:NodeShape ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct: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:description "A unique identifier 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 10 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:BioticExposure . biolink:Book a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Should generally be set to an ontology class defined term for 'book'." ; - sh:order 15 ; - sh:path rdf:type ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + sh:property [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -1420,80 +1411,87 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ 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 16 ; + sh:path rdfs:label ], [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], + sh:order 6 ; + sh:path biolink:license ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct:description ], [ sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; 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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + 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 "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:format ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], + [ 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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], - [ 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 16 ; - sh:path rdfs:label ], + [ sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:order 15 ; + 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 10 ; 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 9 ; + 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 13 ; sh:path biolink:iri ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - 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 2 ; + sh:path biolink:summary ] ; 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 "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 "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 "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:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], + sh:order 19 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 11 ; + 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 13 ; + 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. @@ -1503,6 +1501,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 17 ; 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 21 ; + sh:path biolink:has_attribute ], + [ 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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path dct:description ], [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -1511,60 +1521,50 @@ 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:license ], - [ sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:format ], + sh:order 10 ; + sh:path biolink:rights ], [ sh:description "chapter of a book" ; sh:maxCount 1 ; 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:description "mesh terms tagging a publication" ; - sh:order 7 ; - 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 16 ; - 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: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 "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 "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 14 ; sh:path biolink:full_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 8 ; + sh:path biolink:xref ], + [ sh:order 18 ; + sh:path rdf:type ], [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:order 5 ; 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:order 18 ; - sh:path rdf:type ], - [ 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:maxCount 1 ; - sh:order 10 ; - sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + 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 20 ; - sh:path dct:description ], - [ 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:order 16 ; + 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 19 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path biolink:creation_date ], + [ 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 ; @@ -1581,59 +1581,61 @@ 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:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 36 ; - 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:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:property [ 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 37 ; - sh:path biolink:severity_qualifier ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - 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 27 ; - 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 10 ; - sh:path biolink:aggregator_knowledge_source ], + 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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_attribute ], + 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: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: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:order 20 ; + 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 10 ; + sh:path biolink:aggregator_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 39 ; + sh:path biolink:frequency_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 2 ; + sh:path rdf: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 18 ; sh:path biolink:object_closure ], + [ sh:maxCount 1 ; + sh:order 35 ; + 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 25 ; + sh:path biolink:retrieval_source_ids ], + [ 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 1 ; + 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 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 ; @@ -1644,52 +1646,18 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 7 ; 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 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 "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 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:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ 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: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 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 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 22 ; - sh:path biolink:object_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + 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:order 39 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:severity_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. @@ -1697,125 +1665,113 @@ 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:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears 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:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], - [ sh:description "a point in time" ; + sh:order 21 ; + 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 24 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], + 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 "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 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 "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 19 ; + sh:path biolink:subject_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: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 "A unique identifier 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 description of an entity" ; sh:maxCount 1 ; sh:order 31 ; sh:path dct: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: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 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: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:order 17 ; 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: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:knowledge_source ] ; - sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . - -biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; + sh:order 12 ; + 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 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:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path rdf:subject ], + sh:order 27 ; + 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 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 2 ; + sh:order 0 ; sh:path biolink:sex_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 27 ; - 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:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; 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: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 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 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 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 9 ; + sh:path biolink:primary_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 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:minCount 1 ; sh:order 26 ; - 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: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:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:description "number of things with a particular property" ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 35 ; - 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 19 ; - sh:path biolink:subject_closure ], + sh:order 11 ; + sh:path biolink:timepoint ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + 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 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:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:onset_qualifier ] ; + sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . + +biolink:CausalGeneToDiseaseAssociation 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 22 ; + 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. @@ -1823,92 +1779,155 @@ 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 "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: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: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 "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 "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 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ 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 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 28 ; - sh:path biolink:id ], + sh:order 24 ; + sh:path biolink:object_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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path dct: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 7 ; + sh:path biolink:qualifiers ], [ 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:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 35 ; + sh:path biolink:has_count ], + [ 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 "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 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: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 shown to cause the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + 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 10 ; 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:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], + [ 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: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 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 40 ; + 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 41 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - 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: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:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; 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 8 ; - 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 12 ; sh:path biolink:aggregator_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: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 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 "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 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:order 14 ; + sh:path biolink:original_subject ], + [ 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: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 39 ; - sh:path biolink:severity_qualifier ], - [ sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], + sh:order 2 ; + 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 9 ; + 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 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -1920,75 +1939,71 @@ 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:object_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 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path dct: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 24 ; - sh:path biolink:object_namespace ], + [ sh:maxCount 1 ; + sh:order 37 ; + 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 21 ; - 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:description "Used to hold the 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 40 ; - 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 7 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - 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:order 18 ; + 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:order 41 ; - sh:path biolink:frequency_qualifier ] ; + sh:minCount 1 ; + sh:order 28 ; + 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 19 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:CausalGeneToDiseaseAssociation . biolink:Cell a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the 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:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct: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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "The human readable scientific name for the taxon of the 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 5 ; sh:path biolink:id ], - [ sh:order 8 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:iri ], [ 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 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + [ 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. @@ -1997,48 +2012,58 @@ 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 6 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism 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 3 ; - sh:path biolink:xref ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; 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 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: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 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: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:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + 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: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 19 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + 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 description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2046,175 +2071,193 @@ 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: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 "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: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:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 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: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: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: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 "A human-readable name for an attribute or entity." ; + [ 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: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 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 "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 32 ; + 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 8 ; - sh:path biolink:primary_knowledge_source ], + 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: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: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 0 ; - sh:path rdf: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 "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: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:description "The relationship to the disease" ; 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 "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: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 "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 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 "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 "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 "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: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 "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: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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 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 "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:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:severity_qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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:class biolink:Disease ; - sh:description "disease" ; + [ 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: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:path rdf:object ], + [ 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 "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: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:description "Used to hold the 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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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: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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2222,112 +2265,69 @@ 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 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 "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 "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 relation/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 12 ; - sh:path biolink:original_predicate ], + 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 "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: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: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: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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; 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: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:order 31 ; + 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 20 ; - sh:path biolink:subject_namespace ], + 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: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:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + 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: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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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 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 "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 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 "A human-readable name for an attribute or entity." ; 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 29 ; + sh:path rdfs:label ], + [ 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:order 11 ; - sh:path biolink:original_subject ] ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; @@ -2340,7 +2340,20 @@ 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:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + 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:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + 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`, ... @@ -2349,175 +2362,120 @@ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 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:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - 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 6 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism 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 3 ; - sh:path biolink:xref ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:order 9 ; - sh:path rdfs:label ], + 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 2 ; + sh:path biolink:provided_by ], + [ sh:order 8 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:order 8 ; - sh:path rdf:type ] ; + sh:order 6 ; + 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: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: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 "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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:original_subject ], - [ sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:order 43 ; + sh:path dct:description ], + [ 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 6 ; - sh:path biolink:object_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:order 10 ; + sh:path biolink:causal_mechanism_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: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 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 33 ; - sh:path biolink:subject_namespace ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + [ 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 1 ; - sh:path biolink:subject_part_qualifier ], + sh:order 20 ; + 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 40 ; + 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 39 ; 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 30 ; - 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 25 ; - sh:path biolink:original_predicate ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 16 ; - 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 35 ; - 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 37 ; - sh:path biolink:retrieval_source_ids ], - [ 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: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: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 9 ; + sh:path biolink:object_context_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 29 ; + sh:path biolink:subject_closure ], + [ 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 27 ; - 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 34 ; - 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 22 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:anatomical_context_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:description "a point in time" ; - sh:maxCount 1 ; - sh:order 23 ; - 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 26 ; - 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: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:order 38 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 13 ; + 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 21 ; + 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 30 ; + sh:path biolink:object_closure ], [ 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:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - 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:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path rdf:predicate ], - [ sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 38 ; + 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:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], + sh:order 24 ; + sh:path biolink:original_subject ], [ 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 ; @@ -2525,146 +2483,154 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 15 ; 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 20 ; - 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 31 ; - sh:path biolink:subject_category_closure ], - [ 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: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:order 26 ; + 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 28 ; - sh:path biolink:object_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 21 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 27 ; + 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 19 ; - 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:order 37 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:publications ], - [ 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:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ 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:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path rdf:subject ], + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], [ 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: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: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 human-readable description of an entity" ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path dct:description ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 23 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 42 ; + 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 4 ; - sh:path biolink:subject_context_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 40 ; - sh:path biolink:category ], + sh:order 18 ; + sh:path biolink:publications ], [ 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:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation 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:path biolink:subject_form_or_variant_qualifier ], + [ sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:subject_derivative_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: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:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_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 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 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:order 31 ; + 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 13 ; - sh:path biolink:original_object ], + sh:order 25 ; + 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 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 21 ; + sh:order 34 ; sh:path biolink:object_namespace ], - [ 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: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: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 28 ; + 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 17 ; + 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:order 14 ; sh:path rdf:predicate ], - [ sh:description "a point in time" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:order 16 ; + sh:path biolink:negated ], + [ 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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 41 ; + 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 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 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 "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 "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 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 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: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 ; @@ -2672,190 +2638,220 @@ 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 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 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 "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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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 31 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + 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: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: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:order 26 ; + sh:path biolink:iri ], + [ 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 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: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: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: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 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 "A human-readable name for an attribute or entity." ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + sh:order 30 ; + sh:path dct:description ], [ 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 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: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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct: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:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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:order 27 ; - sh:path biolink:iri ], + 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 32 ; + sh:order 31 ; sh:path biolink:has_attribute ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], - [ 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 "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 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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 30 ; + sh:order 29 ; sh:path rdfs:label ], - [ 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 4 ; - sh:path biolink:negated ], + 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 "a point in time" ; sh:maxCount 1 ; - sh:order 11 ; + 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: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 "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 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:original_subject ], - [ sh:class biolink:GeneOrGeneProduct ; + 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: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: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 "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 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: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 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:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 5 ; + 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 7 ; - sh:path biolink:has_evidence ], + sh:order 19 ; + 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 23 ; + sh:path biolink:subject_label_closure ], [ sh:description "the direction is always from regulator to regulated" ; 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 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 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: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 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 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: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: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 "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:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct: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 "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 ; @@ -2863,45 +2859,49 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape [ 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:nodeKind sh:IRI ; - sh:order 5 ; - 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: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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - 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: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 26 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + 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 13 ; + 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 27 ; + 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 6 ; 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 9 ; - 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 23 ; - sh:path biolink:subject_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 19 ; - 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 28 ; - sh:path biolink:category ] ; + 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 10 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; @@ -2920,16 +2920,9 @@ 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: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 "A unique identifier 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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. @@ -2939,31 +2932,24 @@ 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 "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: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 human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:full_name ], [ 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: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 "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 rdfs:label ], - [ sh:order 11 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ 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 ; @@ -2974,80 +2960,64 @@ 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 8 ; sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ 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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_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 7 ; - sh:path biolink:provided_by ], - [ sh:description "a point in time" ; + sh:order 12 ; + sh:path dct:description ], + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ] ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + 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 2 ; + 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: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: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 10 ; - sh:path rdf:object ], - [ sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ 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: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:property [ 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:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:anatomical_context_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 26 ; - 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 31 ; - 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 16 ; - sh:path biolink:primary_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:order 14 ; + sh:path biolink:has_evidence ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 18 ; + 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:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], + sh:minCount 1 ; + sh:order 9 ; + 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 23 ; - sh:path biolink:object_category ], + sh:order 22 ; + 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 24 ; 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 9 ; - 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 ; @@ -3056,84 +3026,74 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 36 ; 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: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 13 ; - 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 17 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + 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 5 ; - sh:path biolink:object_part_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:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ 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 21 ; - 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 25 ; - sh:path biolink:object_closure ], + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 38 ; sh:path dct: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:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 29 ; - 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 14 ; - sh:path biolink:has_evidence ], - [ 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 ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:order 6 ; + sh:path biolink:object_context_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 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:order 28 ; + 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 22 ; - 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 15 ; - 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 34 ; - sh:path biolink:iri ], + sh:order 23 ; + 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 26 ; + 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 33 ; sh:path biolink:id ], - [ sh:description "a point in 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 31 ; + sh:path biolink:object_label_closure ], + [ 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:order 18 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 10 ; + 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 16 ; + 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 35 ; + sh:path biolink: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 30 ; 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 19 ; - 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 28 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -3141,36 +3101,76 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path rdf:subject ], - [ 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 11 ; - 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 35 ; - sh:path biolink:category ], + sh:order 29 ; + 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 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ 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: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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_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 32 ; - sh:path biolink:retrieval_source_ids ], + sh:order 3 ; + sh:path biolink:subject_context_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 20 ; - sh:path biolink:original_predicate ] ; + 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 19 ; + 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 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: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: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: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: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: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:targetClass biolink:ChemicalGeneInteractionAssociation . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; @@ -3182,100 +3182,122 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation 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, typically (but not always) undesirable effect." ; 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 "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; 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:order 0 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:maxCount 1 ; - sh:order 27 ; - 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 10 ; - sh:path biolink:aggregator_knowledge_source ], + 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct: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 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:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + [ 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:BlankNode ; - sh:order 1 ; - 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 18 ; - sh:path biolink:object_closure ], + 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: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 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: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 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: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 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: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 22 ; - 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 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:order 14 ; - 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 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:minCount 1 ; + sh:order 26 ; + 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 8 ; + 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 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: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 "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: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:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; + [ 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:timepoint ], - [ 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:order 14 ; + 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 4 ; - sh:path biolink:negated ], + sh:order 9 ; + 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 21 ; 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 18 ; + sh:path biolink:object_closure ], + [ 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 "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 ; @@ -3283,30 +3305,56 @@ 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 "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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - 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:order 31 ; + sh:path dct: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: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 19 ; - 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:order 6 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + 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 27 ; + sh:path biolink:iri ] ; + 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: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 16 ; - sh:path biolink:object_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: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 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 12 ; + 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 7 ; 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 21 ; + sh:path biolink:subject_namespace ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 30 ; @@ -3316,109 +3364,70 @@ 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:FDA_adverse_event_level ], - [ 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 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 2 ; - 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: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:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; 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: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 "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 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 "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 16 ; - 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 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 "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: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 "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 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:order 3 ; + 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 8 ; sh:path biolink: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 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: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: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 "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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 27 ; - 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:order 13 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 1 ; + sh:path rdf:subject ], [ 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 "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 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 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 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 point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3426,156 +3435,129 @@ 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 "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 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 "A unique identifier 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: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 "Used to hold the 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:order 16 ; + 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 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: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 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 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 13 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:nodeKind sh:IRI ; + 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:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - 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:order 9 ; + 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 21 ; - sh:path biolink:subject_namespace ], + sh:order 14 ; + sh:path biolink:original_object ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 31 ; - sh:path dct:description ] ; + sh:path dct: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 "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: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 "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: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: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 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + 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 "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - 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: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: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:order 12 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; 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:order 30 ; + sh:path dct:description ], + [ sh:description "a point in time" ; 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 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 "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 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: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 "a point in time" ; + 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 10 ; - sh:path biolink:timepoint ], + 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: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: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 namespace 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: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 "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: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:order 8 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -3583,59 +3565,77 @@ biolink:ChemicalToChemicalAssociation 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: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: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: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 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 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:maxCount 1 ; + 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 5 ; - sh:path biolink:publications ], + sh:order 18 ; + 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 4 ; + 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 22 ; + 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 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: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: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 31 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:order 19 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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: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 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 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 6 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:ChemicalToChemicalAssociation . biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; @@ -3649,54 +3649,69 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; THEN C1 derives-into C2 <>""" ; 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:description "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - 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: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: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 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: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 14 ; + 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 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 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 27 ; + 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 4 ; + sh:path biolink:negated ], + [ 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: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 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:class biolink:ChemicalEntity ; + sh:description "the upstream chemical entity" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:object_namespace ], + 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 "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 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: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 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:order 15 ; + 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 6 ; - sh:path biolink:publications ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct: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. @@ -3704,166 +3719,120 @@ 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: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 unique identifier 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 "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: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 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 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:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - 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 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: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 "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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], + sh:order 32 ; + 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 7 ; 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 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: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 16 ; - 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 27 ; - sh:path biolink:iri ], + sh:order 20 ; + 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 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: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 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: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:class biolink:ChemicalEntity ; sh:description "the downstream chemical entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path rdf:object ] ; - 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: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: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 13 ; - sh:path biolink:original_object ], + sh:order 9 ; + 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:description "Used to hold the 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_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: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 25 ; + 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:order 22 ; 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:class biolink:Publication ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:timepoint ] ; + 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: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:description "a human-readable description of an entity" ; + [ 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 dct:description ], + 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 "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: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:DiseaseOrPhenotypicFeature ; + sh:description "the disease or phenotype that is affected by the chemical" ; 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: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 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:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -3871,84 +3840,115 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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: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 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: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 "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 description of an entity" ; sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ 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: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 "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 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:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + 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: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 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:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "the disease or phenotype that is affected by the chemical" ; + [ 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: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: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: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 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 "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 "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:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + 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:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + 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 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 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:ChemicalToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; @@ -3960,99 +3960,82 @@ 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 description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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 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 "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: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: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 "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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 7 ; - sh:path biolink: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: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 "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: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:Pathway ; - sh:description "the pathway that is affected by the chemical" ; + 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:minCount 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 "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 unique identifier 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: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: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: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. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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: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 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 ; @@ -4064,142 +4047,165 @@ 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: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: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 "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 "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 "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: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 7 ; + sh:path biolink: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: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:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; - 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 description of an entity" ; + 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 "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 dct: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:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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: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:has_attribute ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + 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 IRI for an entity. This is determined by the id using expansion rules." ; 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:order 26 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ] ; + 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:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ 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:maxCount 1 ; + sh:order 8 ; + 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: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 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 4 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ 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: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:iri ], + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_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 5 ; + sh:path biolink:xref ], [ sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ] ; + sh:path biolink:license ] ; 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:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 11 ; + sh:path dct:description ], [ 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:order 4 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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 ; 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:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -4211,45 +4217,58 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 2 ; 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:description "a long-form human readable name for a thing" ; + [ sh: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:full_name ], + 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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:ClinicalCourse . 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:class biolink:Attribute ; + 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ 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 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 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 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 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. @@ -4262,54 +4281,33 @@ 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 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 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 4 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct: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 3 ; - sh:path biolink:id ] ; + sh:path rdfs:label ] ; 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 human readable scientific name for the taxon of the entity." ; + 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 2 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct: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 human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:order 8 ; - 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:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + [ 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. @@ -4324,50 +4322,55 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t 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:maxCount 1 ; + sh:minCount 1 ; + sh:order 5 ; + 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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; 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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:ClinicalFinding . biolink:ClinicalIntervention a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 6 ; - sh:path 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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], [ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 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 description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + sh:order 7 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_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. @@ -4377,40 +4380,43 @@ 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 1 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ 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 7 ; - sh:path rdfs:label ] ; + 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 0 ; + sh:path biolink:provided_by ] ; 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: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:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:order 10 ; + 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ 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 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. @@ -4420,68 +4426,63 @@ 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:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + 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:order 11 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], [ 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 10 ; - 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 "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 "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 long-form human readable name for a thing" ; + 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 8 ; - sh:path biolink:full_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 7 ; - sh:path biolink:xref ] ; + sh:order 4 ; + sh:path biolink:iri ] ; 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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 9 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct: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: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 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 "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: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 ; @@ -4489,51 +4490,52 @@ 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 "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 description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct: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: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 "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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]+$" ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ClinicalModifier . biolink:ClinicalTrial a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4543,108 +4545,84 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 5 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ], + [ sh:description "A 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 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 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: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 0 ; + sh:path biolink:provided_by ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct: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 0 ; - sh:path biolink:provided_by ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:ClinicalTrial . biolink:CodingSequence a sh:NodeShape ; sh:closed true ; 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 11 ; - sh:path biolink:xref ], - [ sh:description "" ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], + sh:order 2 ; + sh:path rdfs:label ], [ 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:has_attribute ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_metabolite ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:maxCount 1 ; sh:order 16 ; 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: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 3 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:is_metabolite ], + [ 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 "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:order 15 ; - sh:path rdf:type ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - 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 7 ; - sh:path biolink:max_tolerated_dose ], - [ 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 long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], + [ sh:order 15 ; + 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. @@ -4654,10 +4632,32 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; 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 10 ; + sh:path biolink:provided_by ], + [ sh:description "" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:iri ] ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + 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 3 ; + sh:path biolink:id ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct:description ] ; sh:targetClass biolink:CodingSequence . biolink:Cohort a sh:NodeShape ; @@ -4668,19 +4668,25 @@ biolink:Cohort a sh:NodeShape ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:order 8 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct: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:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 9 ; + sh:order 1 ; 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 "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4690,42 +4696,62 @@ 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 "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 6 ; - sh:path biolink:iri ], + sh:order 9 ; + 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: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 5 ; - 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:description "The human readable scientific name for the taxon of the entity." ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ] ; + sh:order 10 ; + sh:path dct:description ], + [ sh:order 8 ; + sh:path rdf:type ] ; 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 "a long-form human readable name for a thing" ; + sh:property [ 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ 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 5 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], + [ 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 8 ; + 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. @@ -4735,132 +4761,155 @@ 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 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: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 8 ; - sh:path biolink:iri ], [ 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 "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 11 ; + 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 7 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:order 10 ; - 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:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ] ; + sh:order 1 ; + sh:path biolink:rights ] ; 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 "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 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 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: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 "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ 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 10 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ 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 5 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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: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 9 ; - 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: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: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 6 ; - 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 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ComplexChemicalExposure . 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:class biolink:ChemicalMixture ; - sh: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 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:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:id ], + [ 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 ; + sh:order 18 ; + sh:path biolink:has_attribute ], + [ 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 13 ; + sh:path biolink:iri ], + [ sh:class biolink:ChemicalMixture ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:is_supplement ], - [ 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 11 ; + sh:path biolink:full_name ], + [ 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 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:order 15 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct:description ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; @@ -4879,74 +4928,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; 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 13 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path rdfs:label ], - [ 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 18 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an 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 17 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:order 15 ; - 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - 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 "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ] ; + sh:path biolink:provided_by ] ; 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: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: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 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. @@ -4956,23 +4955,10 @@ 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 5 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ 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 13 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 12 ; + sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; @@ -4981,52 +4967,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 11 ; 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 7 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 12 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:creation_date ], [ 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ] ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:order 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:ConceptCountAnalysisResult . biolink:ConfidenceLevel a sh:NodeShape ; sh:closed true ; 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives 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 description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:order 10 ; - 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 unique identifier 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 "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + [ 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5036,282 +5028,290 @@ 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 2 ; + sh:path biolink:format ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_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 4 ; - 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 3 ; sh:path biolink:creation_date ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ 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:order 8 ; sh:path biolink:iri ], - [ 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 "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ] ; 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 description of an entity" ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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:order 29 ; + 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: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: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: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 "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: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: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:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - 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 "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 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: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: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: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 "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 "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 "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 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:nodeKind sh: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: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: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 "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 description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; 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: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 "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 19 ; + sh:path biolink:object_category_closure ], + [ 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 "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Agent ; + sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; 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: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 2 ; + sh:path rdf:object ], + [ 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: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 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:targetClass biolink:ContributorAssociation . biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; 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 "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:publications ], + sh:order 21 ; + 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 25 ; + sh:path biolink:subject_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 7 ; + 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 22 ; + 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 17 ; + sh:path biolink:subject_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 "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: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 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 "A unique identifier 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 "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: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:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ 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:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the 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 10 ; + 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 12 ; + 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 19 ; + 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 40 ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to correlate with the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path dct:description ], + [ 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 "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 ( "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 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: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 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: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 "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 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 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:Disease ; + sh:description "disease" ; 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: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:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 5 ; + sh:path rdf:object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -5323,53 +5323,22 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:sex_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:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to correlate with the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - 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 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: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 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: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 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: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:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:object_direction_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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5377,53 +5346,88 @@ 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: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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + 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 18 ; - sh:path biolink:object_category ], + 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 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 37 ; + sh:path biolink:has_quotient ], + [ 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: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 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 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 41 ; - sh:path biolink:frequency_qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path rdfs:label ], + [ sh:description "a point in time" ; + 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:maxCount 1 ; sh:order 29 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + 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 33 ; - sh:path dct:description ] ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ] ; 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 "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_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 7 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:source_web_page ], + [ 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:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -5432,117 +5436,113 @@ biolink:DatasetSummary a sh:NodeShape ; [ sh:maxCount 1 ; sh:order 1 ; sh:path schema1:logo ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct: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:maxCount 1 ; - sh:order 3 ; - sh:path biolink:rights ], + sh:order 4 ; + 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:maxCount 1 ; - sh:order 2 ; - sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 4 ; - 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 11 ; - 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 5 ; 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 6 ; - sh:path biolink:provided_by ], + [ sh:maxCount 1 ; + sh:order 2 ; + 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 7 ; + sh:path biolink:xref ], [ sh:order 12 ; sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:source_web_page ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ] ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + 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:maxCount 1 ; + 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 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:maxCount 1 ; + sh:minCount 1 ; + sh:order 10 ; + 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:maxCount 1 ; sh:order 5 ; sh:path biolink:format ], + [ sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:rights ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 15 ; sh:path dct: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 10 ; - 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:license ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:order 13 ; + sh:path rdf:type ], [ 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 3 ; - 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. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:class biolink:DatasetDistribution ; + [ sh:class biolink:Dataset ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ], + sh:order 0 ; + sh:path biolink:has_dataset ], [ 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 long-form human readable name for a thing" ; + [ sh:class biolink:DatasetDistribution ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path dct:distribution ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 4 ; - sh:path biolink:rights ], - [ sh:class biolink:Dataset ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_dataset ], - [ 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 14 ; - sh:path rdfs:label ], - [ sh:order 13 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:ingest_date ] ; @@ -5552,56 +5552,85 @@ 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 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: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. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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]+$" ], [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 3 ; sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""" ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + 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 9 ; + sh:path biolink:has_attribute ], [ 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: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 1 ; + sh:path biolink:xref ] ; 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: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: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:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:order 11 ; + 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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_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 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -5614,39 +5643,12 @@ 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:timepoint ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct: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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], [ 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 "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 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:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -5659,13 +5661,11 @@ 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 biolink:has_quantitative_value ], - [ sh:order 11 ; - sh:path rdf:type ], - [ 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 "A unique identifier 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:DiseaseOrPhenotypicFeatureExposure . biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; @@ -5683,39 +5683,22 @@ 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 "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 high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + 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:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; + 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: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:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; 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: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:minCount 1 ; 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 0 ; + sh:path rdf:subject ], [ sh:class biolink:GeneticInheritance ; sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; @@ -5723,96 +5706,48 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape 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 "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: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: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 "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 "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:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + 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 30 ; - sh:path dct:description ], - [ 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 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 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 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: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: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 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 14 ; - sh:path biolink:subject_category ], + 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: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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -5823,315 +5758,380 @@ 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: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: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:order 31 ; + 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: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_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 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 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 "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 "if set to true, then the association is negated i.e. is not true" ; 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:order 3 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; 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. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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 "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: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: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:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct: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 "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:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; - 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: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: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 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:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category_closure ] ; + 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: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: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 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 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 "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:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 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 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: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 20 ; - sh:path biolink:subject_namespace ], + 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 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: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:order 18 ; + 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 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 "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: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 "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: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:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . - -biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:DiseaseToEntityAssociationMixin . - -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 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: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: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:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; 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: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 "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 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: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:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ 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: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: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:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; 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: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: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 "A unique identifier 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 "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: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 8 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + +biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:DiseaseToEntityAssociationMixin . + +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 "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ 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 14 ; - sh:path biolink:subject_category ], + 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: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: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: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: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 7 ; - 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: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 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: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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; 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:order 31 ; + 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:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; + 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 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: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:Disease ; - sh:description "disease class" ; + [ 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - 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: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:order 21 ; - sh:path biolink:object_namespace ], + 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 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: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 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 description of an 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 dct:description ], - [ 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. + 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: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 ; + 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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 "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 13 ; - sh:path biolink:original_object ] ; + sh:order 7 ; + sh:path biolink: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:Disease ; + sh:description "disease class" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:DiseaseToExposureEventAssociation . biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -6143,15 +6143,22 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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 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: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 27 ; - 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 6 ; - sh:path biolink:publications ], + sh:order 37 ; + sh:path biolink:severity_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. @@ -6159,110 +6166,87 @@ 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 "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 33 ; - 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 8 ; - sh:path biolink:knowledge_source ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:has_percentage ], - [ 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 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: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 "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 "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:frequency_qualifier ], + sh:order 30 ; + 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 26 ; 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 23 ; - sh:path biolink:subject_label_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: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 11 ; - 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 24 ; - 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 10 ; - 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 18 ; + 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 7 ; sh:path biolink:has_evidence ], - [ 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 "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 9 ; + 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 23 ; + 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 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:order 6 ; + 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:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:subject_category ], + 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 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 "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 34 ; + 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 17 ; + 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 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 "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:has_count ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct: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: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 "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:nodeKind sh:IRI ; - sh:order 16 ; - 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 24 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Disease ; sh:description "disease class" ; sh:maxCount 1 ; @@ -6270,72 +6254,87 @@ 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 "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 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 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 "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 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 "total number of things in a particular reference set" ; + [ 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: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 17 ; - sh:path biolink:subject_closure ], + sh:order 22 ; + 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 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + 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 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:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ sh:description "equivalent to has quotient multiplied by 100" ; 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:order 36 ; + sh:path biolink:has_percentage ], + [ 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_object ] ; + 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: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: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 "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 35 ; + sh:path biolink:has_quotient ] ; 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: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:NamedThing ; - sh:description "connects an attribute to a value" ; + 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 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:path biolink:xref ], + [ 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 4 ; - sh:path biolink:has_qualitative_value ], + 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 ; @@ -6343,23 +6342,6 @@ biolink:DrugExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_attribute_type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ 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: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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct: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. @@ -6369,22 +6351,40 @@ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; 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 8 ; - sh:path biolink:xref ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ 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 point in time" ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:order 11 ; - 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 2 ; + sh:path rdfs:label ], + [ 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -6396,63 +6396,53 @@ 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:order 15 ; + sh:property [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], + [ sh:order 15 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct: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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_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 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: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 "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ 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 "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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path rdfs:label ], + sh:order 17 ; + sh:path dct:description ], [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "executive summary of a publication" ; + sh:order 8 ; + 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 2 ; - sh:path biolink:summary ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], + sh:order 9 ; + sh:path biolink:creation_date ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], + [ sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], + [ 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 16 ; + 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 10 ; + 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. @@ -6462,14 +6452,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ 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 12 ; 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 7 ; + sh:path biolink:rights ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; @@ -6482,35 +6482,19 @@ 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: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 subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + 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 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. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:order 15 ; + sh:path biolink:object_category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Drug ; sh:description "the drug that is an interactor" ; sh:maxCount 1 ; @@ -6518,177 +6502,181 @@ 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 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 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 "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 "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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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: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 subject namespace 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:has_attribute ], + [ 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:order 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + 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 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:order 8 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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: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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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: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 "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 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: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 21 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product that is affected by the drug" ; + 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 "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], + 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: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: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 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 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: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: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 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 14 ; + sh:path biolink:subject_category ] ; 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:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_attribute_type ], + sh:order 10 ; + sh:path biolink:full_name ], + [ sh:order 12 ; + 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 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 8 ; - sh:path biolink:provided_by ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ], - [ 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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ 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: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 5 ; 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 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 3 ; sh:path rdfs:label ], - [ sh:order 12 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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 8 ; + sh:path biolink:provided_by ], + [ 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:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 1 ; + 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. @@ -6698,189 +6686,171 @@ 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:description "a long-form human readable name for a thing" ; + [ 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:full_name ] ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct: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 9 ; + sh:path biolink:xref ], + [ 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:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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 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 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + 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:order 38 ; - sh:path biolink:has_percentage ], - [ 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 37 ; - sh:path biolink:has_quotient ], + 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:maxCount 1 ; sh:order 14 ; sh:path biolink:original_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: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 point in time" ; + [ 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:timepoint ], + sh:order 29 ; + 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 27 ; + sh:path biolink:retrieval_source_ids ], [ 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:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path rdf:type ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], + [ 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: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: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: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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path dct: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: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: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 ( "increased" "upregulated" "decreased" "downregulated" ) ; 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:order 1 ; + sh:path biolink:object_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 26 ; + sh:path biolink:object_label_closure ], + [ 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:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + 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 30 ; + sh:path biolink: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:description "A human-readable name for an attribute or entity." ; + [ 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 32 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ 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 "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 "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 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:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ 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: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 3 ; - 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 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 10 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path dct:description ], + sh:order 4 ; + 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 12 ; + 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 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 "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 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 "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:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_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 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: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: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:description "a point in time" ; sh:maxCount 1 ; - sh:order 0 ; - 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 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:order 13 ; + 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 ; @@ -6890,25 +6860,53 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; 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: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 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 human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + 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 15 ; + sh:path biolink:original_predicate ], + [ 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:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ] ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ] ; 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 "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:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 5 ; sh:path dct:description ], + [ sh:order 3 ; + 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 ; @@ -6921,101 +6919,117 @@ 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 2 ; sh:path biolink:category ], - [ 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 "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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 4 ; sh:path rdfs:label ], - [ 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:targetClass biolink:Entity . biolink:EntityToDiseaseAssociation 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:property [ 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: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: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:negated ], + [ 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 15 ; - sh:path biolink:subject_category ], - [ 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:order 3 ; + sh:path rdf:object ], + [ 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 14 ; - sh:path biolink:original_object ], - [ 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 0 ; + sh:path biolink:FDA_approval_status ], + [ 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 "A unique identifier 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 3 ; - sh:path rdf:object ], + sh:order 5 ; + 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 16 ; + sh:path biolink:object_category ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 29 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], + [ 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: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 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 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 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 "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: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 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: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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 14 ; + 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 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 "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 26 ; - sh:path biolink:id ], - [ 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 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:order 0 ; - sh:path biolink:FDA_approval_status ], + 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. @@ -7023,91 +7037,77 @@ 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 "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 human-readable description of an entity" ; + [ 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 31 ; - sh:path dct:description ], + 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:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ 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 30 ; - 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 6 ; - 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 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: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: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: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:order 22 ; + 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 27 ; - sh:path biolink:iri ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:original_predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; 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: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 23 ; + 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 24 ; 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 1 ; - sh:path rdf:subject ] ; + sh:order 11 ; + 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 17 ; + 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 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 21 ; + sh:path biolink:subject_namespace ] ; 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:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + 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:order 2 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + 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:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the 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:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:severity_qualifier ] ; + sh:order 2 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; @@ -7152,11 +7152,35 @@ biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; biolink:EntityToPhenotypicFeatureAssociation 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: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: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 2 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + 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 5 ; + 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 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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], [ 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 ; @@ -7164,115 +7188,86 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; 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 7 ; + sh:path biolink:has_evidence ], + [ 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: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 6 ; + 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 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 "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: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 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 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: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: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 "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 "a point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], - [ 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 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: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 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 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 "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: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 "" ; - 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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], - [ 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 "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: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: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: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: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 22 ; - 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 19 ; - sh:path biolink:subject_category_closure ], + 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 "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: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 "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 30 ; + 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. @@ -7280,55 +7275,43 @@ 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 28 ; 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 "a point in time" ; + sh:maxCount 1 ; + sh:order 11 ; + 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 25 ; - sh:path biolink:retrieval_source_ids ], + 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 "A unique identifier 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 "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 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: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:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_count ], - [ sh:maxCount 1 ; - sh:order 3 ; - 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 7 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:BiologicalSex ; + sh:property [ 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: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 ; @@ -7339,31 +7322,34 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:severity_qualifier ], + [ sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 1 ; + 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 6 ; + sh:path biolink:onset_qualifier ], [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 2 ; - sh:path biolink:has_total ] ; + sh:path biolink:has_total ], + [ 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:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_quotient ] ; 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:order 11 ; - 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 "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 8 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; @@ -7381,14 +7367,20 @@ 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:full_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 8 ; + sh:path biolink:xref ], + [ 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 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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + [ sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -7396,15 +7388,6 @@ 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: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 value in this node property represents the knowledge provider that created or assembled the node 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 ], @@ -7413,28 +7396,60 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct: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: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:EnvironmentalExposure . biolink:EnvironmentalFeature a sh:NodeShape ; sh:closed true ; 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 "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: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 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 description of an entity" ; 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. + sh:order 8 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_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 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: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`, ... @@ -7443,75 +7458,72 @@ 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: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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ 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:full_name ] ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:EnvironmentalFeature . biolink:EnvironmentalFoodContaminant 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:description "" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ 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: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 8 ; - sh:path biolink:id ], + sh:order 2 ; + 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 6 ; + sh:path biolink:xref ], + [ sh:order 11 ; + sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:full_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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], + sh:order 12 ; + sh:path rdfs:label ], + [ 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 14 ; + 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 4 ; sh:path biolink:has_chemical_role ], - [ sh:order 11 ; - 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:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; 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 9 ; + 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:description "A unique identifier 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7520,42 +7532,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 10 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:EnvironmentalFoodContaminant . biolink:EnvironmentalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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:property [ 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 1 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ 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 ; @@ -7565,13 +7549,22 @@ biolink:EnvironmentalProcess a sh:NodeShape ; 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 0 ; - 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 human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct: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 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. @@ -7580,7 +7573,14 @@ 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:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_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 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; @@ -7602,23 +7602,22 @@ 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 long-form human readable name for a thing" ; + 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: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 long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ 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:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct: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: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. @@ -7628,168 +7627,169 @@ 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct: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: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 "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 "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 "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 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 21 ; - sh:path biolink:object_namespace ], + 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: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: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: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 "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 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 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 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: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: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 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 "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 "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: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 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 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: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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 14 ; + sh:path biolink:subject_category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct: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 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:object_category ], + 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: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: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: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: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 ; 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:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_evidence ], + sh:order 31 ; + 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 27 ; + sh:path biolink: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 "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: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:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + 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 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: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 ; @@ -7801,7 +7801,15 @@ 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 "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 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: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 "A unique identifier 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 ; @@ -7811,42 +7819,66 @@ biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], - [ 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 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - 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 7 ; - 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 9 ; - 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 18 ; + 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 22 ; 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 23 ; + 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:description "Used to hold the 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:subject_category_closure ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 16 ; + 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 11 ; + 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 5 ; - 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 25 ; - sh:path biolink:object_label_closure ], + sh:minCount 1 ; + sh:order 3 ; + 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 14 ; + sh:path biolink:original_predicate ], + [ 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 "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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 31 ; sh:path rdfs:label ], + [ 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 1 ; + sh:path biolink:temporal_context_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:timepoint ], + [ 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 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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -7854,27 +7886,15 @@ 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: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 "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: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:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; 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:qualifiers ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 5 ; + sh:path biolink:negated ], [ 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 ; @@ -7882,298 +7902,323 @@ 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: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 "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: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:subject_category ], - [ 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: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 "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path dct: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:maxCount 1 ; - sh:order 14 ; - 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 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:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 30 ; - sh:path rdf:type ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:order 7 ; + 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 20 ; + 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 0 ; - sh:path biolink:population_context_qualifier ], + sh:order 17 ; + sh:path biolink:object_category ], + [ 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 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + 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: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: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:order 21 ; + sh:path biolink:object_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 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:timepoint ], + sh:order 32 ; + sh:path dct: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 15 ; 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 23 ; - 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 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:object_category ] ; + sh:order 33 ; + 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 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 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:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct: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: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: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: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: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: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:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], [ 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: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 "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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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 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 "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:order 15 ; + 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 21 ; + sh:path biolink:subject_namespace ], [ 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: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 "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 point in time" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:timepoint ], + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ 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 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 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: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: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:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject" ; + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:onset_qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:order 34 ; + sh:path biolink:has_total ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path dct: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 17 ; - sh:path biolink:subject_closure ], + 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:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ 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: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: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 "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: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 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: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 "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: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: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 1 ; - 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 21 ; - 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 26 ; - sh:path biolink:id ], [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 33 ; sh:path biolink:has_count ], - [ 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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 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 25 ; - 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:order 19 ; + 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:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], + 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:description "A human-readable name for an attribute or entity." ; + [ 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path rdfs:label ] ; + sh:minCount 1 ; + sh:order 26 ; + 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 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: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 "The value in this node property represents the knowledge provider that created or assembled the node 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 10 ; - sh:path biolink:xref ], + sh:property [ 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 "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:order 15 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + 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 12 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path rdfs:label ], + [ 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct:description ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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:maxCount 1 ; - sh:order 13 ; - sh:path biolink:iri ], + sh:order 7 ; + 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 10 ; + sh:path biolink:xref ], + [ 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: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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 13 ; + 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. @@ -8183,61 +8228,73 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; 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: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 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 "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 16 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ] ; + sh:targetClass biolink:Food . + +biolink:FoodAdditive 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:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:description "" ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "a long-form human readable name for a thing" ; 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 15 ; + sh:path biolink:full_name ], + [ 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:order 11 ; sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 14 ; 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:description "" ; + sh:maxCount 1 ; + 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "" ; + sh:in ( "over_the_counter" "prescription" ) ; sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + 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 8 ; + sh:path biolink:id ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; + sh:order 13 ; sh:path dct:description ], - [ 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 12 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Food . - -biolink:FoodAdditive 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:path rdfs:label ], + [ 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -8245,64 +8302,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 10 ; 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: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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ 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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_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 6 ; - sh:path biolink:xref ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - 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 8 ; - sh:path biolink:id ], - [ sh:order 11 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 3 ; - 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 9 ; - 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:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - 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 2 ; - sh:path biolink:max_tolerated_dose ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:FoodAdditive . biolink:FrequencyQualifierMixin a sh:NodeShape ; @@ -8318,116 +8318,156 @@ 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:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_count ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_quotient ], - [ 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 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:path biolink:has_percentage ], + [ 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: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:class biolink:OntologyClass ; + sh:property [ 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: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 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 "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: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: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 "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 "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: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: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 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 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: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:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_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:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 30 ; + sh:path dct: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 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 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 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: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 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: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 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 "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 description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ 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: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 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: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:class biolink:OntologyClass ; sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; @@ -8435,69 +8475,29 @@ biolink:FunctionalAssociation 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: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: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: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: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: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: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:order 6 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; 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 "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 "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: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 8 ; - 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:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:path biolink:has_attribute ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; @@ -8507,20 +8507,23 @@ biolink:Fungus a sh:NodeShape ; 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 11 ; - sh:path biolink:has_attribute ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], - [ 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 5 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path rdfs:label ], + [ sh:order 8 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 ], @@ -8533,173 +8536,119 @@ 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 "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 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 9 ; - sh:path rdfs:label ] ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ] ; sh:targetClass biolink:Fungus . biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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 relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ 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 15 ; - 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 21 ; - 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 8 ; - sh:path biolink:publications ], - [ sh:description "number of things with a particular property" ; + sh:order 0 ; + sh:path biolink:subject_aspect_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:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_count ], + sh:order 41 ; + sh:path biolink:frequency_qualifier ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 33 ; sh:path dct: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 20 ; - sh:path biolink:object_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path rdfs:label ], - [ 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 "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:nodeKind sh:BlankNode ; - sh:order 3 ; - 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 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 28 ; - 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 23 ; - sh:path biolink:subject_namespace ], + 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:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + 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 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 "a point in time" ; sh:maxCount 1 ; sh:order 13 ; 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 40 ; + sh:path biolink:onset_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 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: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:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_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:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - 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 14 ; - sh:path biolink:original_subject ], - [ 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: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 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 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 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 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:order 21 ; + 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 22 ; + 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 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:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:maxCount 1 ; 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: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 "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 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:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - 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:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:onset_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:SeverityValue ; sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; sh:maxCount 1 ; @@ -8710,61 +8659,112 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; 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:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting 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 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - 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 30 ; - sh:path biolink:category ], + sh:order 34 ; + 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 7 ; - sh:path biolink:qualifiers ] ; + sh:order 18 ; + sh:path biolink:object_category ], + [ 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 "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 3 ; + sh:path rdf: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 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: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: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 "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + 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 8 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + 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 12 ; + 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 16 ; + 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 26 ; + sh:path biolink:object_label_closure ] ; 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:DiseaseOrPhenotypicFeature ; + 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: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 3 ; sh:path biolink:phenotypic_state ], - [ 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: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:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + [ 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:targetClass biolink:GeneExpressionMixin . biolink:GeneGroupingMixin a sh:NodeShape ; @@ -8781,602 +8781,602 @@ biolink:GeneGroupingMixin a sh:NodeShape ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Disease ; + 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 17 ; + 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 16 ; + 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 11 ; + sh:path biolink:knowledge_source ], + [ 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: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 human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 33 ; + 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 28 ; - 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:order 9 ; + 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 26 ; + 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:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + 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 10 ; + sh:path biolink:has_evidence ], + [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:has_quotient ], - [ 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 37 ; + 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 20 ; + sh:path biolink:subject_closure ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 25 ; - 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:order 2 ; + 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 8 ; + 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:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:minCount 1 ; + sh:order 29 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:frequency_qualifier ], + sh:order 14 ; + sh:path biolink:timepoint ], + [ 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:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_quotient ], [ 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 "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ 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:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ 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 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 "Used to hold the 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 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: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 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 "number of things with a particular property" ; sh:maxCount 1 ; sh:order 36 ; 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: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:subject_namespace ], + sh:order 25 ; + 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 12 ; + 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 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 "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 "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - 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 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 29 ; - sh:path biolink:id ], + sh:order 5 ; + 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 22 ; - 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 40 ; - sh:path biolink:severity_qualifier ], - [ 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 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: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:description "Used to hold the 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 "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:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ 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:order 2 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path rdf:subject ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 34 ; sh:path dct: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 31 ; - 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: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 "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 17 ; - 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:order 24 ; + sh:path biolink:subject_namespace ], + [ 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 16 ; - sh:path biolink:original_predicate ], + sh:order 42 ; + sh:path biolink:frequency_qualifier ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:subject_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 27 ; - 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 30 ; - 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 26 ; - sh:path biolink:subject_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 8 ; - sh:path biolink:qualifiers ], - [ sh:description "total number of things in a particular reference set" ; + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_total ], - [ 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 original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 39 ; + sh:path biolink:has_percentage ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 7 ; + sh:path biolink:negated ], [ 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: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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 32 ; - sh:path rdf:type ], - [ 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:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 39 ; - 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: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 3 ; - sh:path biolink:sex_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path rdfs:label ] ; + sh:order 22 ; + sh:path biolink:subject_category_closure ] ; 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 "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:property [ 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 "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 2 ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeneProductIsoformMixin . biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; 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 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: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 34 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + 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: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 9 ; - sh:path biolink:has_evidence ], + sh:order 39 ; + sh:path biolink:severity_qualifier ], + [ 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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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 17 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:order 4 ; + 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 15 ; + sh:path biolink:original_predicate ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 33 ; sh:path dct:description ], - [ 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: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 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 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: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 18 ; - 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 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ 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:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:order 9 ; + 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: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: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:maxCount 1 ; - sh:order 37 ; - sh:path biolink:has_quotient ], - [ 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: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: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 "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:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:sex_qualifier ], + 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 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: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: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 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 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: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 "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: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 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 "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:maxCount 1 ; - 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:order 10 ; - sh:path biolink: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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:severity_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 unique identifier 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: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:targetClass biolink:GeneToDiseaseAssociation . - -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation 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 phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; - 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: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:maxCount 1 ; - sh:order 16 ; - 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 30 ; - 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:order 34 ; + sh:path biolink:has_attribute ], + [ sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_total ], + [ 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:nodeKind sh:IRI ; - 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:order 2 ; + sh:path biolink:sex_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:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + 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 23 ; + 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 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:description "a human-readable description of an entity" ; + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path dct: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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + 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 point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + 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 19 ; + 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 12 ; + sh:path biolink:aggregator_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 41 ; sh:path biolink:frequency_qualifier ], - [ 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: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:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - 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 8 ; - sh:path biolink:publications ], + sh:order 0 ; + 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: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 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:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + [ 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 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + 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 24 ; + 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 39 ; - sh:path biolink:severity_qualifier ], - [ sh:description "total number of things in a particular reference set" ; + sh:order 18 ; + 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 ; - sh:order 36 ; - sh:path biolink:has_total ], - [ 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:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 40 ; + sh:path biolink:onset_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:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + 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 34 ; - sh:path biolink:has_attribute ], + 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:maxCount 1 ; sh:order 10 ; sh:path biolink: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 0 ; + sh:path biolink:subject_aspect_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 "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_percentage ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 13 ; 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 11 ; - sh:path biolink:primary_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 2 ; sh:path biolink:sex_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: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: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 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:has_percentage ], + sh:order 1 ; + sh:path biolink:object_direction_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:maxCount 1 ; + sh:order 37 ; + sh:path biolink:has_quotient ], + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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: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 7 ; - 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 14 ; - sh:path biolink:original_subject ], + 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 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 "if set to true, then the association is negated i.e. is not true" ; + [ 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 6 ; - sh:path biolink:negated ], - [ 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 37 ; - sh:path biolink:has_quotient ], + sh:order 41 ; + 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:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path dct: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 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 17 ; + sh:path biolink:subject_category ], [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 35 ; sh:path biolink:has_count ], + [ 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: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 18 ; 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: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:object_namespace ], + sh:order 14 ; + 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 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: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 unique identifier 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: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 relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 29 ; + sh:path biolink:iri ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 3 ; + sh:path rdf:subject ], + [ 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 4 ; - sh:path rdf:predicate ] ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + 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 27 ; + 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 24 ; + 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 7 ; + 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 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:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . biolink:GeneToEntityAssociationMixin a sh:NodeShape ; @@ -9388,248 +9388,215 @@ 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 "a human-readable description of an entity" ; + 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 19 ; + 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 32 ; - sh:path dct:description ], - [ sh:description "expression relationship" ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - 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:subject_category ], - [ 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:maxCount 1 ; - sh:order 14 ; - 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 25 ; - 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 22 ; - 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 26 ; - 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 7 ; - 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:order 4 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_object ], + sh:order 32 ; + sh:path dct: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 24 ; + 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 28 ; 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 29 ; + 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 18 ; 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 "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_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 17 ; - sh:path biolink:object_category ], + sh:order 6 ; + 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 13 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "can be used to indicate magnitude, or also ranking" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:quantifier_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 19 ; - sh:path biolink:object_closure ], - [ 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 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - 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 24 ; - 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 9 ; 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 27 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path rdfs:label ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 30 ; + 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 5 ; 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 20 ; - 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 13 ; - 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 21 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; + [ 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 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + 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 4 ; - 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:qualifiers ], + sh:order 8 ; + 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 11 ; 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 29 ; - sh:path biolink:category ], [ 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 "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 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:primary_knowledge_source ], - [ 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:order 16 ; + 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 26 ; + 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 23 ; sh:path biolink:object_namespace ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 31 ; + 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 0 ; - sh:path biolink:stage_qualifier ] ; - 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 "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:description "a human-readable description of an entity" ; + sh:order 17 ; + sh:path biolink:object_category ], + [ 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 "A unique identifier 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:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ 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 0 ; + sh:path biolink:stage_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 22 ; + 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 19 ; + sh:order 21 ; 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: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 24 ; - sh:path biolink:retrieval_source_ids ], + sh:order 20 ; + 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 15 ; + 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:order 7 ; 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 "a point in time" ; + [ sh:description "expression relationship" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 3 ; + 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 25 ; + sh:path biolink:object_label_closure ] ; + 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 "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 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: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 "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 2 ; - sh:path rdf:object ], + 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: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 "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 human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + 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: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 "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: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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -9637,237 +9604,270 @@ 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: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 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: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 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 4 ; + sh:path biolink:qualifiers ], + [ 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:order 11 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + 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: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 "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; 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:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; 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 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 "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: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 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 "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: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: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: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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - 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:order 30 ; + sh:path dct:description ] ; 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: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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_attribute ], + [ 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:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + 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 30 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ 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: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 object 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 ], + [ 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:order 17 ; - sh:path biolink:original_object ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ 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 "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 33 ; + 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 20 ; 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 9 ; - 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:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - 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 22 ; - sh:path biolink:subject_category_closure ], + sh:order 14 ; + 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 26 ; + 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:order 29 ; 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 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 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 IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:iri ], [ 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 "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 33 ; - sh:path rdfs:label ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ 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: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 "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:nodeKind sh:BlankNode ; - sh:order 6 ; - 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 31 ; - 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 27 ; - 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 10 ; - 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 8 ; - sh:path biolink:qualifiers ], + sh:order 25 ; + 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 7 ; 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 26 ; - 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 28 ; - sh:path biolink:retrieval_source_ids ], - [ 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: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 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: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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path dct: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 25 ; - 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 13 ; - 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:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 32 ; + 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 11 ; + 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 16 ; 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 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:primary_knowledge_source ], + sh:order 17 ; + 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 13 ; + sh:path biolink:aggregator_knowledge_source ], [ 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: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 4 ; - sh:path rdf:subject ], + sh:order 6 ; + sh:path rdf: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 5 ; sh:path rdf:predicate ], - [ 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 14 ; - sh:path biolink:timepoint ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 32 ; - sh:path rdf:type ] ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ 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 3 ; + sh:path biolink:phenotypic_state ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path dct: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 31 ; + 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 23 ; + 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 9 ; + 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 22 ; + 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 28 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:GeneToGeneCoexpressionAssociation . biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; @@ -9877,55 +9877,56 @@ biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; 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 "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 description of an entity" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "membership of the gene in the given gene family." ; + sh:order 30 ; + sh:path dct:description ], + [ 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: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: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 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: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 "membership of the gene in the given gene family." ; 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 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: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 20 ; - sh:path biolink:subject_namespace ], + 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 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 "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: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: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 ; @@ -9933,139 +9934,113 @@ biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; 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: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: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 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 11 ; - 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + 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 "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:description "Used to hold the 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:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path biolink:object_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: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 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: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: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 "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 "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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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: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 26 ; + sh:path biolink:iri ], + [ 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 "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 "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 "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 7 ; - sh:path biolink: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:order 12 ; + sh:path biolink:original_predicate ] ; 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 "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 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 description of an entity" ; + 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 30 ; - sh:path dct: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: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: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: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 ; - 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: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 ; @@ -10073,82 +10048,111 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; 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 "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 "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - 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 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path rdf:object ], [ sh:description "homology relationship type" ; sh:maxCount 1 ; 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 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 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 unique identifier 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: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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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: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 15 ; - sh:path biolink:object_category ], + 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: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:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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 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: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: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 "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 "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 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 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: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 "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10156,41 +10160,44 @@ 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: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 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 "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 6 ; + sh:path biolink:has_evidence ] ; 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: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: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 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:order 21 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + 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: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 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: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: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 ; @@ -10198,45 +10205,31 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; 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 "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 "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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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: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 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 "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:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ 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 ; @@ -10247,43 +10240,31 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; [ 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 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 "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: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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + sh:order 30 ; + sh:path dct: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: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: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 "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:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -10294,39 +10275,58 @@ 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 "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: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 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 "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: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 description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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: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:Attribute ; - sh:description "connects any entity to an attribute" ; + 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: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 18 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:GeneToGeneProductRelationship . biolink:GeneToGoTermAssociation 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:property [ 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10334,387 +10334,366 @@ 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 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: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:description "a point in time" ; + 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 10 ; - sh:path biolink:timepoint ], + 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 "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 "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 "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: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: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 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 24 ; - sh:path biolink:retrieval_source_ids ], + 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 "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: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 "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; + sh:minCount 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: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:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 13 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], + 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 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 "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 human-readable description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct:description ], - [ 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: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 "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 "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: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:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the 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 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 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: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 "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 "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: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 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: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 0 ; - sh:path rdf:subject ] ; + 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: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: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 "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 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 "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: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: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 "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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; + 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 "A unique 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 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: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:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + 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 "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 high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + 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: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 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:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - 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: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: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:has_attribute ], + [ sh:description "a human-readable description of an entity" ; 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:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 30 ; + sh:path dct: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 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 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:object_category ], + 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 "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: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: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: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: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: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 "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 "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 "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 "a point in time" ; sh:maxCount 1 ; 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 "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; 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: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:minCount 1 ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:GeneToPathwayAssociation . biolink:GeneToPhenotypicFeatureAssociation 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:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - 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:property [ 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:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "a human-readable description of an entity" ; + sh:order 23 ; + 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:order 33 ; - sh:path dct: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: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: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: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 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 22 ; - sh:path biolink:object_category_closure ], - [ 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 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 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 "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:order 9 ; + sh:path biolink:has_evidence ], [ 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: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 "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 5 ; - sh:path rdf:object ], + sh:order 15 ; + 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 4 ; sh:path rdf:predicate ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + [ 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 38 ; - sh:path biolink:has_percentage ], - [ 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 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: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 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:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:severity_qualifier ], + sh:order 22 ; + 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 18 ; + 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 21 ; 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: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 1 ; - 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: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. @@ -10722,47 +10701,75 @@ 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 37 ; - 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 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: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 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path dct:description ], [ 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 IRI for an entity. This is determined by the id using expansion rules." ; + [ 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: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 "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 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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + 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 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:iri ], + 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 0 ; sh:path biolink:sex_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: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: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 8 ; - 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 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:order 5 ; + 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:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:severity_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 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; @@ -10770,39 +10777,20 @@ 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 "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:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears 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:order 16 ; + 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 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:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 8 ; + 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 9 ; - sh:path biolink:has_evidence ], - [ 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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - 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 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:order 27 ; + 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 24 ; @@ -10810,36 +10798,33 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:order 36 ; - sh:path biolink:has_total ] ; + sh:path biolink:has_total ], + [ sh:description "a point in time" ; + 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:maxCount 1 ; + 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:targetClass biolink:GeneToPhenotypicFeatureAssociation . 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 "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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ 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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -10849,65 +10834,78 @@ 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path dct: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 1 ; + sh:path biolink:id ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; + 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 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:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:order 9 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path rdfs:label ] ; 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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNode ; - sh:order 8 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + 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 11 ; + 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 rdfs:label ], - [ sh:order 15 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + 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 9 ; 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:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 6 ; + sh:order 4 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 12 ; + 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 biolink:timepoint ], + 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. @@ -10917,51 +10915,53 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; 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 2 ; + sh:path biolink:has_biological_sequence ], + [ 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 8 ; + sh:path biolink:has_quantitative_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 6 ; + 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: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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 16 ; sh:path dct: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 12 ; - 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 7 ; - sh:path biolink:has_attribute_type ], [ 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 10 ; - sh:path biolink:iri ], - [ 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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ] ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:order 15 ; + sh:path rdf:type ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; @@ -10982,352 +10982,346 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + 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 25 ; + 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 27 ; 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 21 ; - sh:path biolink:subject_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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "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 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:order 6 ; + 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:nodeKind sh:IRI ; - sh:order 19 ; - 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 22 ; - 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:order 16 ; + sh:path biolink:original_subject ], + [ 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 13 ; - sh:path biolink:primary_knowledge_source ], + sh:order 4 ; + sh:path biolink:phase ], [ 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 24 ; - sh:path biolink:object_category_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:order 23 ; + 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 28 ; + sh:path biolink:object_label_closure ], + [ 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 0 ; + sh:path biolink:start_interbase_coordinate ], + [ sh:description "A unique identifier 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 "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + 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 5 ; - sh:path rdf:subject ], + sh:order 20 ; + 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 21 ; + sh:path biolink:subject_closure ], [ 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 "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: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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ 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:order 35 ; + sh:path dct:description ], + [ 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 4 ; - sh:path biolink:phase ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + 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 29 ; + sh:path biolink:retrieval_source_ids ], [ 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 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: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 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: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 "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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path dct:description ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - 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 31 ; - sh:path biolink:iri ], - [ 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 subject 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 16 ; - 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:order 34 ; + sh:path rdfs:label ], + [ 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 30 ; - 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 17 ; - 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 32 ; - sh:path biolink:category ], - [ 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 0 ; - sh:path biolink:start_interbase_coordinate ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], [ 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 "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 "a point in time" ; - sh:maxCount 1 ; - sh:order 15 ; - 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: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 18 ; - sh:path biolink:original_object ], + sh:order 12 ; + 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 23 ; - 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: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 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 24 ; + 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 14 ; + 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:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 19 ; + 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 31 ; + 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 17 ; + 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 22 ; + 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 13 ; + sh:path biolink:primary_knowledge_source ], [ 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 "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 34 ; - 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 14 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:order 8 ; + sh:path biolink:negated ] ; sh:targetClass biolink:GenomicSequenceLocalization . biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + 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 34 ; + sh:path biolink:frequency_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 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 "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 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: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 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:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:onset_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 23 ; + sh:path biolink:object_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:description "The relationship to the disease" ; + 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: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: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:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; + [ sh:description "A unique 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 0 ; - sh:path rdf:subject ], + 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: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 "The relationship to the disease" ; + [ sh:class biolink:Disease ; + sh:description "disease" ; 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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 "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 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: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 "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 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 description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the 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: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: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: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: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 "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: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: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 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 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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink: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:order 30 ; + sh:path dct: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:class biolink:Disease ; - sh:description "disease" ; + [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "A genotype 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: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 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 "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 "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:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ 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:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + 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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; @@ -11338,142 +11332,148 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; 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: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 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: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 "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:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ 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: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 "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: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 "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a human-readable description of an entity" ; 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:order 30 ; + sh:path dct: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 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: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 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:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + 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: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 34 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf: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:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "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 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: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: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: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: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:class biolink:Disease ; + sh:description "a disease that is associated with that genotype" ; 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 "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:minCount 1 ; + sh:nodeKind sh:IRI ; + 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ 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 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: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 31 ; - sh:path biolink:has_attribute ], - [ 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 IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 26 ; - sh:path biolink:iri ] ; + 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:targetClass biolink:GenotypeToDiseaseAssociation . biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; @@ -11485,77 +11485,60 @@ 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: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:property [ 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: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 "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 15 ; - sh:path biolink:object_category ], + 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: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: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 description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct: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: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: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 "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 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 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 "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: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 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. @@ -11567,12 +11550,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t 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 "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: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: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:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -11580,170 +11577,157 @@ 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 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 "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: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: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 14 ; + sh:path biolink:subject_category ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:timepoint ], - [ sh:class biolink:Gene ; - sh:description "gene implicated in genotype" ; + [ 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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:maxCount 1 ; - sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + 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 "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: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: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 "the relationship type used to connect genotype to gene" ; + 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: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: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:description "A unique identifier 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 description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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: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 "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 "child genotype" ; + [ 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 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: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 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 "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 "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:primary_knowledge_source ], + 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: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 "A human-readable name for an attribute or entity." ; + 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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: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 24 ; - sh:path biolink:retrieval_source_ids ], + 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: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:Genotype ; + sh:description "child genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category_closure ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 "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: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 "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 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 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: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:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -11751,59 +11735,68 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; 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 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 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 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 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:order 8 ; + sh:path biolink:primary_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 "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 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: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: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: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: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 "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 "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 30 ; 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 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: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: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 2 ; - sh:path rdf:predicate ], + sh:order 20 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Genotype ; sh:description "genotype that is associated with the phenotypic feature" ; sh:maxCount 1 ; @@ -11811,27 +11804,61 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path dct:description ], [ 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:EvidenceType ; - sh:description "connects an association to an instance of supporting 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 26 ; + sh:path biolink:id ], + [ 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 "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 32 ; + sh:path biolink:has_attribute ], + [ 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 14 ; - sh:path biolink:original_object ], + sh:nodeKind sh:IRI ; + sh:order 37 ; + 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 22 ; + 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 10 ; sh:path biolink:aggregator_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 39 ; + sh:path biolink:frequency_qualifier ], + [ 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: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 "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 "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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -11839,39 +11866,53 @@ 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 28 ; 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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct:description ], + [ sh:maxCount 1 ; + sh:order 35 ; + 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 20 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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: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 27 ; - 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: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:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:object_category ], + sh:order 38 ; + sh:path biolink:onset_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 2 ; + sh:path rdf:predicate ], [ 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 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 21 ; - 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:order 27 ; + 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 38 ; - sh:path biolink:onset_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 8 ; - sh:path biolink:knowledge_source ], + sh:order 16 ; + sh:path biolink:object_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 ; @@ -11879,212 +11920,148 @@ 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 "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: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 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 0 ; sh:path biolink:sex_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 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 "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 "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: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 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:order 11 ; + sh:path biolink:timepoint ], [ 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: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 unique identifier 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 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 "number of things with a particular property" ; 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:class biolink:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; + sh:order 33 ; + 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:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], - [ sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:has_quotient ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - sh:path rdf:type ], + 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 "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:has_count ] ; + sh:path biolink:publications ] ; 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: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 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 description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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 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 relationship type used to connect genotype to gene" ; - 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 "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:property [ sh:description "a human-readable description of an 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:order 30 ; + sh:path dct: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 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: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:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; + [ 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 "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 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: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 "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 "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 15 ; sh:path biolink:object_category ], - [ sh:description "a point in time" ; + [ 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:timepoint ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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 "the relationship type used to connect genotype to gene" ; 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: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:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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: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:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -12092,30 +12069,53 @@ 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 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 "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: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: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 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 13 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ 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: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 31 ; - 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 biolink:publications ], + [ sh:description "a point in time" ; 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 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:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; @@ -12126,25 +12126,6 @@ biolink:GenotypicSex a sh:NodeShape ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ 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 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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct: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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12154,8 +12135,11 @@ 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:order 10 ; - 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:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -12167,100 +12151,146 @@ 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 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: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 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:order 10 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct: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: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: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: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:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:order 11 ; + 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:has_attribute_type ], + sh:order 13 ; + 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 10 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ 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 "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 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 8 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ 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 unique identifier 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 "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 11 ; - 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: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 "a long-form human readable name for a thing" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_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. + sh:minCount 1 ; + 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 10 ; + sh:order 7 ; 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 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 7 ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "latitude" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:latitude ], [ 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: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 "a long-form human readable name for a thing" ; + 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], @@ -12268,15 +12298,8 @@ biolink:GeographicLocation a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], - [ 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:order 8 ; + 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 ], @@ -12284,45 +12307,17 @@ biolink:GeographicLocation a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:longitude ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "A unique identifier 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 "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 "latitude" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:latitude ], - [ sh:order 8 ; - 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:order 9 ; + sh:path rdfs:label ] ; 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: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:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 10 ; sh:path rdfs:label ], @@ -12330,25 +12325,11 @@ biolink:GeographicLocationAtTime a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:longitude ], - [ 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: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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "latitude" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:latitude ], [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -12361,38 +12342,46 @@ 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 4 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:timepoint ] ; + sh:path biolink:timepoint ], + [ sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:description "latitude" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:latitude ] ; 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 2 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 9 ; - 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:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + 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. @@ -12402,90 +12391,101 @@ 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "may often be an organism 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 6 ; sh:path biolink:iri ], - [ sh:order 8 ; - sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + 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 "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + 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:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ] ; + sh:path dct: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:order 8 ; + 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: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 "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 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: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 2 ; sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 11 ; - sh:path dct:description ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 10 ; sh:path rdfs:label ], + [ 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct: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 1 ; 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 10 ; + sh:order 3 ; sh:path rdfs:label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -12496,10 +12496,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:Hospitalization 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 4 ; - 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. @@ -12509,36 +12508,37 @@ 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: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 "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct: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 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:order 6 ; + sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_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 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 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:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -12551,31 +12551,46 @@ 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: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 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 6 ; - 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 9 ; sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct: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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 6 ; + sh:path biolink:iri ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_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: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 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. @@ -12585,31 +12600,21 @@ 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 "A unique identifier 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 "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the 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: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:description "A human-readable name for an attribute or entity." ; + 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 "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], @@ -12617,130 +12622,107 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; 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: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 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 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 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 6 ; + sh:path biolink:has_evidence ], + [ 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:order 31 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct:description ], + [ 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: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: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 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: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: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 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 "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: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: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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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 "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 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_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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: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 "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 "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:description "if set to true, then the association is negated i.e. is not true" ; + [ 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:order 3 ; - sh:path biolink:negated ], + 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 "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 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: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 "a point in time" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:object_category ], + [ 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 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:publications ], + 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: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:maxCount 1 ; @@ -12748,40 +12730,59 @@ 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: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 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 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: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: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:InformationContentEntityToNamedThingAssociation . 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 "The human readable scientific name for the taxon of the entity." ; - 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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path dct: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 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 human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - 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:order 1 ; + 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: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. @@ -12791,15 +12792,14 @@ 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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_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 3 ; sh:path biolink:xref ], - [ 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 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 2 ; sh:path biolink:provided_by ], @@ -12807,128 +12807,130 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 9 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ] ; + sh:order 4 ; + sh:path biolink:full_name ] ; 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: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 "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 "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 18 ; - 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 14 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], + sh:order 21 ; + sh:path dct: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: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 1 ; - sh:path biolink:iso_abbreviation ], + [ sh:order 19 ; + sh:path rdf:type ], [ sh:description "keywords tagging a publication" ; sh:order 7 ; sh:path biolink:keywords ], - [ sh:order 19 ; - 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 20 ; 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: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 16 ; - 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 "a long-form human readable name for a thing" ; + [ 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:full_name ], + sh:order 17 ; + sh:path biolink:iri ], [ sh:description "mesh terms tagging a publication" ; sh:order 8 ; sh:path biolink:mesh_terms ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:issue ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "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 1 ; + sh:path biolink:iso_abbreviation ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:full_name ], + [ sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:license ], [ sh:maxCount 1 ; sh:order 11 ; sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ] ; + sh:order 6 ; + sh:path biolink:summary ], + [ 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 "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:maxCount 1 ; + sh:order 12 ; + 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 18 ; + 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:minCount 1 ; + sh:order 16 ; + sh:path biolink:id ] ; 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: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 4 ; - sh:path biolink:provided_by ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + 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:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:order 10 ; + sh:path rdf:type ], + [ 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 8 ; + 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. @@ -12938,38 +12940,36 @@ 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 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: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 long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], + [ 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 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: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 4 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + 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:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; - sh:path dct:description ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ] ; + sh:path dct:description ] ; sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; @@ -12981,27 +12981,11 @@ biolink:MacromolecularComplex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh: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:full_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 8 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + 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 ; @@ -13009,54 +12993,90 @@ 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 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 "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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:order 8 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:order 9 ; sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 2 ; + 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:path biolink:in_taxon ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct: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: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: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: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 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 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 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: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: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 "A unique identifier 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 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 "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:BiologicalProcess ; sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; @@ -13064,170 +13084,119 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; 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: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 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:description "a point in time" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:knowledge_source ], + 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 "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: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: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 "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: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: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: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 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:order 26 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; 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:order 30 ; + sh:path dct: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: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: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 "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 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: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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + 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:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ 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:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path rdf:subject ], + 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 "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 5 ; - 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 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:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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 26 ; - sh:path biolink:iri ], + 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: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:path biolink:negated ] ; 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 "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 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 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: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 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:order 8 ; + sh:path biolink:primary_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 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: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 relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:original_predicate ], + sh:order 30 ; + sh:path dct:description ], [ sh:class biolink:CellularComponent ; sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; @@ -13235,19 +13204,39 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; 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 "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 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 "A human-readable name for an attribute or entity." ; + [ 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 "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 29 ; - sh:path rdfs:label ], + 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. @@ -13255,16 +13244,18 @@ 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 human-readable description of an entity" ; + [ 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 30 ; - sh:path dct:description ], + 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: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:object_category ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -13272,62 +13263,71 @@ 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 "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ 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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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 31 ; - sh:path biolink:has_attribute ], + 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: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 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 "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 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 20 ; - sh:path biolink:subject_namespace ], - [ 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 "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: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 "An IRI for an entity. This is determined by the id using expansion rules." ; + 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 26 ; - sh:path biolink:iri ], + 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: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 "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 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: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 "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:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; @@ -13340,66 +13340,43 @@ 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: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 description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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: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:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + 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 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:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - 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 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 "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: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: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:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:order 3 ; - 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:minCount 1 ; + sh:nodeKind sh:BlankNode ; + 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: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:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "a human-readable description of an entity" ; 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 31 ; - sh:path biolink:has_attribute ], + sh:order 30 ; + sh:path dct: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 ; @@ -13408,11 +13385,26 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; [ 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: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 19 ; - sh:path biolink:object_category_closure ], + 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 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 ; @@ -13422,15 +13414,25 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "a point in 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 "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: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 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: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:retrieval_source_ids ], + 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13438,65 +13440,71 @@ 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: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: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: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:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 24 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNode ; - 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: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 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:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; + [ 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: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: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: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 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: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 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 7 ; - sh:path biolink:knowledge_source ] ; + sh:order 26 ; + sh:path biolink:iri ] ; 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; 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 "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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -13506,42 +13514,34 @@ 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], - [ sh:order 8 ; - 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:order 1 ; + sh:path rdfs:label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct: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: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 human readable scientific name for the taxon of the 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 1 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ] ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:order 8 ; + 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:targetClass biolink:Mammal . biolink:MappingCollection a sh:NodeShape ; @@ -13559,190 +13559,89 @@ 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: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: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: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 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 "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:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + 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: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 "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 "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 "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: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 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 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 "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 "derivation relationship" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf: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:MaterialSample ; - sh:description "the material sample being described" ; + [ sh:description "A human-readable name for an attribute or entity." ; 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:order 29 ; + 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 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: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: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 original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + 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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 IRI for an entity. This is determined by the id using expansion rules." ; + 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 26 ; - sh:path biolink:iri ], + 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 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 "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 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 "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 30 ; - sh:path dct:description ] ; - 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 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: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:path dct: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 20 ; - sh:path biolink:subject_namespace ], + 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 "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 "A unique identifier 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 ; @@ -13751,73 +13650,105 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; [ 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: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 "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: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 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: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: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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:publications ] ; + 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 "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 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: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:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + 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 "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: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: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 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. @@ -13825,34 +13756,103 @@ 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: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 "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 "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 "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:description "a point in time" ; - sh:maxCount 1 ; - 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 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: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:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + [ 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 "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:class biolink:MaterialSample ; + sh:description "the material sample being described" ; 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: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 "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 description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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: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:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; @@ -13864,43 +13864,71 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 8 ; - sh:path biolink:available_from ], + 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 9 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:is_metabolite ], [ sh:description "" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - 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 12 ; - sh:path biolink:provided_by ], + sh:order 18 ; + sh:path dct:description ], + [ sh:description "The human readable scientific name for the taxon of the 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 14 ; + 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 11 ; sh:path biolink:has_chemical_role ], - [ 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 14 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:order 16 ; + 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:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 12 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:trade_name ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 8 ; + sh:path biolink:available_from ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ 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. @@ -13910,46 +13938,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 15 ; 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 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path rdfs:label ], - [ sh:order 16 ; - sh:path rdf:type ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:is_metabolite ], - [ 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 17 ; - 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 19 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:full_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 9 ; - 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 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 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; @@ -13962,44 +13962,46 @@ 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: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:description "a human-readable description of an entity" ; + sh:property [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], + 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: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 "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 "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 3 ; - 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 27 ; - sh:path biolink:category ], + 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: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: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 "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: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 ; @@ -14007,112 +14009,128 @@ 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 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 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: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: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 6 ; - sh:path biolink:has_evidence ], + 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 "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 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 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:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:original_object ], + sh:order 30 ; + sh:path dct: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 "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: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: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 "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: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 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: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: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 "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:minCount 1 ; - 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: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 7 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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 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: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: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: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: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 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: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 "a human-readable description of an entity" ; + sh:property [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ 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: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:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct:description ], @@ -14121,96 +14139,88 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:publications ], - [ 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 29 ; - sh:path rdfs:label ], + 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: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: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: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: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: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 "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 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: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: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 7 ; - sh:path biolink:knowledge_source ], + 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: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 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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 ; sh:minCount 1 ; - sh:order 25 ; - sh:path biolink:id ], + 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: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 high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:original_subject ], + 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 point in time" ; sh:maxCount 1 ; 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 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 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 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 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 "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. @@ -14218,39 +14228,29 @@ 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: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: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: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 1 ; - sh:path rdf:predicate ], + 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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: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:order 20 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -14262,28 +14262,66 @@ 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: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: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 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 "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: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: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 "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 "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:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_attribute ], - [ 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: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:order 20 ; + 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 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. @@ -14291,35 +14329,33 @@ 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 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: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: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:order 29 ; - sh:path rdfs:label ], + 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: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 description of an entity" ; sh:maxCount 1 ; sh:order 30 ; @@ -14329,119 +14365,69 @@ 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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: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 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: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: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 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 "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 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: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 "A unique identifier 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 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: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: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 "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 "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: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: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:description "A unique identifier 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: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 "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + 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:drug_regulatory_status_world_wide ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 11 ; + sh:path biolink:full_name ], [ sh:description "" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - 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:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ 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:order 15 ; - sh:path rdf:type ], + 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. @@ -14451,42 +14437,49 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_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:nodeKind sh:IRI ; + sh:order 4 ; + 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 13 ; + sh:path biolink:iri ], [ 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 "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 16 ; - 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 "The value in this node property represents the knowledge provider that created or assembled the node 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + 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:class biolink:ChemicalMixture ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:is_supplement ], + [ sh:order 15 ; + sh:path rdf:type ], [ 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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 17 ; @@ -14495,7 +14488,14 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; - sh:path biolink:id ] ; + 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 "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:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -14508,115 +14508,95 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; 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:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 "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: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 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 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: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: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 11 ; - sh:path biolink:original_subject ], - [ 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 "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 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 human-readable description of an 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 30 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:primary_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 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; + 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 10 ; - sh:path biolink:timepoint ], + 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: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: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 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: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 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: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: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: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 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. @@ -14624,40 +14604,92 @@ 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: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: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 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: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:subject_category_closure ], + 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 "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 "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: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:order 29 ; + sh:path rdfs:label ], + [ 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:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . biolink:NoncodingRNAProduct 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 "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:is_metabolite ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + 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 11 ; + 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 5 ; + 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... @@ -14666,92 +14698,83 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 15 ; 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 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 19 ; + sh:path biolink:has_attribute ], + [ sh:order 16 ; + sh:path rdf:type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:full_name ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path rdfs:label ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 8 ; 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 12 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct: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 "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: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 11 ; - sh:path biolink:has_chemical_role ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path rdfs:label ], [ 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 17 ; sh:path rdfs:label ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:trade_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:is_toxic ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 6 ; - 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 14 ; - sh:path biolink:iri ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:path biolink:iri ] ; + 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:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:order 16 ; - sh:path rdf:type ], + 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 12 ; + 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 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 "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 5 ; - sh:path biolink:id ] ; - 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 6 ; + sh:path biolink:iri ], + [ 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. @@ -14761,69 +14784,37 @@ 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 "A unique identifier 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: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 2 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:order 8 ; - sh:path rdf:type ], [ 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 "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 long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:full_name ] ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct: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: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 "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 6 ; - 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:property [ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + 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. @@ -14833,71 +14824,63 @@ 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 4 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - 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 ; - 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 3 ; + 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 10 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:full_name ], + [ 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 4 ; + sh:path biolink:xref ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 2 ; 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh: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:full_name ] ; + 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 "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ] ; 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 11 ; - sh:path rdfs:label ], - [ sh:order 10 ; + sh:property [ sh:order 10 ; sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_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 4 ; 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 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. @@ -14907,27 +14890,44 @@ 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 "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 7 ; sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 1 ; + 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:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + 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 2 ; + sh:path biolink:format ], + [ 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 8 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; @@ -14940,51 +14940,54 @@ 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + 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 "A unique identifier 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:order 10 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct: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: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: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 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 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 6 ; + 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: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:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; @@ -14994,13 +14997,10 @@ 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:full_name ], - [ 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:order 0 ; + sh:path rdfs:label ] ; sh:targetClass biolink:OrganismAttribute . biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; @@ -15012,120 +15012,11 @@ 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 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 "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; + 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 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ 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 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: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 "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: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:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - 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: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 "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 "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: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 "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 "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 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. @@ -15133,95 +15024,176 @@ 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 "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 "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:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + 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: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 "Used to hold the 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 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 "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 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 19 ; - sh:path biolink:object_category_closure ] ; - 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:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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 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: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:NamedThing ; + sh:description "the environment in which the organism occurs" ; 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 "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: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 "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: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: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 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:description "a point in time" ; + sh:maxCount 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 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:maxCount 1 ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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: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: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 "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: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 description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 "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 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: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:class biolink:OrganismTaxon ; sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -15229,17 +15201,31 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; 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: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:description "A unique identifier 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 "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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -15247,65 +15233,79 @@ 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 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 "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: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 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:description "a human-readable description of an entity" ; + 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 30 ; - sh:path dct:description ], + 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 "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 "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: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 "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:description "A human-readable name for an attribute or entity." ; + 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 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:order 11 ; + sh:path biolink:original_subject ], + [ 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 18 ; - sh:path biolink:subject_category_closure ], + 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: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 14 ; - sh:path biolink:subject_category ] ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; @@ -15317,59 +15317,65 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; 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: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 "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: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 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 "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: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 "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: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 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 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 "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 31 ; sh:path dct:description ], + [ sh:description "the environment in which the two taxa interact" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:associated_environmental_context ], [ 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 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 "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. @@ -15377,166 +15383,175 @@ 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 "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 "the environment in which the two taxa interact" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], - [ 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 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: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:subject_category_closure ], - [ 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:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; 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:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + 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 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: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 "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ 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 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 5 ; - sh:path biolink:qualifiers ], + 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: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: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:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + [ 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 ; + 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: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: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: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 "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:description "a human-readable description of an entity" ; + 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 30 ; - sh:path dct: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 "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:OrganismTaxon ; + sh:description "the more general taxon" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:subject_namespace ], + 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: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 "A unique identifier 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 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: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 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 "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ 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 1 ; - sh:path rdf:predicate ], + 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: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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 description of an entity" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 30 ; + sh:path dct:description ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; + sh:description "the more specific taxon" ; 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:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 0 ; + 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:order 29 ; - sh:path rdfs:label ], + 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 ; @@ -15545,32 +15560,10 @@ 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: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: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:description "A human-readable name for an attribute or entity." ; 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 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 "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: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 ], @@ -15578,105 +15571,136 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t 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: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:OrganismTaxon ; - sh:description "the more specific taxon" ; - 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 0 ; - sh:path rdf:subject ], + 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 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 "Used to hold the 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 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 unique identifier 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: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: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:order 24 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . biolink:OrganismToOrganismAssociation 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: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: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: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 "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: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: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 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: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 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 "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 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: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 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 24 ; - sh:path biolink:retrieval_source_ids ], + 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 "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 "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 1 ; - sh:path rdf:predicate ], + 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 "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 29 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ 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: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:order 30 ; - sh:path dct:description ], + 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:class biolink:IndividualOrganism ; sh:description "An association between two individual organisms." ; sh:maxCount 1 ; @@ -15684,77 +15708,53 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; 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 "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: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 description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:object_category ], + sh:order 30 ; + sh:path dct: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 "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: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 "A unique identifier 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: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: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: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 0 ; - sh:path rdf:subject ], + 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: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: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 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 "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 ; @@ -15764,107 +15764,69 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - 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 ; - sh:order 32 ; - 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 33 ; - 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 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct:description ], - [ 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: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 "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 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 "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: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 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: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 ; - 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:minCount 1 ; 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: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 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: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: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 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 relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path rdf:predicate ], - [ 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: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 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: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 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 "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 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. @@ -15872,271 +15834,307 @@ 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: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: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: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: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 "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: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 human-readable name for an attribute or entity." ; + [ 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 rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:iri ], + sh:order 30 ; + sh:path dct:description ], + [ 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 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 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: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 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: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 "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 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 point in time" ; + [ 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: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:description "a point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], + 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 "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 "interaction relationship 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 "A unique identifier 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: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: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 "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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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: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: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 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: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 31 ; - sh:path biolink:has_attribute ], + 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: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 "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:description "interaction relationship type" ; 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: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 "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 19 ; - sh:path biolink:object_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: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 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:order 0 ; + sh:path rdf:subject ], + [ 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: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 "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 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: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: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 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: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: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 description of an entity" ; + [ sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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 "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 3 ; + sh:path biolink:negated ], + [ 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:order 11 ; - sh:path biolink:original_subject ] ; + sh:minCount 1 ; + 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: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: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 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 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: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 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 19 ; + 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 13 ; 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 12 ; - 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 7 ; sh:path biolink:has_evidence ], - [ 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 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 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:order 8 ; + sh:path biolink: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 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:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category_closure ], + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], + [ sh:description "interaction relationship type" ; + 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:description "Used to hold the 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_closure ], - [ sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:order 15 ; + 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 21 ; + sh:path biolink:subject_namespace ], + [ 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:order 26 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path dct: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 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. @@ -16144,116 +16142,100 @@ 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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 29 ; - 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 27 ; + 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 16 ; + sh:path biolink:object_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:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_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: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: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 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 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:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_attribute ], - [ sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - 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 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 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 point in time" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:subject_namespace ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + 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:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 22 ; + sh:path biolink:object_namespace ], + [ 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 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + 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 14 ; 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:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + sh:order 4 ; + 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 31 ; - sh:path dct:description ], - [ 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:order 12 ; + 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 18 ; + sh:path biolink:object_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 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: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 1 ; - sh:path rdf:subject ], - [ 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 20 ; + sh:path biolink:object_category_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: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 3 ; - sh:path rdf:object ] ; + 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: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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], - [ 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 12 ; - sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], - [ sh:order 15 ; - 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. + 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`, ... @@ -16267,48 +16249,66 @@ 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:authors ], - [ 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path rdfs:label ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 13 ; + sh:path biolink:iri ], + [ sh:order 15 ; + sh:path rdf:type ], + [ 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 12 ; + 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 7 ; - sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct: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: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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], [ sh:description "keywords tagging a publication" ; sh:order 3 ; 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 13 ; - 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:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:rights ], + [ 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 18 ; + 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 "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; - sh:path biolink:summary ] ; + sh:path biolink:summary ], + [ 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 16 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct:description ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -16321,36 +16321,20 @@ 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: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: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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct: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:class biolink:Attribute ; + 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: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:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], + 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 ; @@ -16359,33 +16343,49 @@ biolink:PathologicalAnatomicalExposure 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 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: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:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNode ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:order 11 ; - 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 "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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 9 ; - sh:path biolink:full_name ] ; + sh:path biolink:full_name ], + [ sh:order 11 ; + 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:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; @@ -16398,44 +16398,44 @@ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:order 8 ; + sh:property [ sh:order 8 ; sh:path rdf:type ], [ 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:description "The human readable scientific name for the taxon of the 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 human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:full_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:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path dct: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 "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + 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 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 6 ; + 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. @@ -16462,18 +16462,32 @@ 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: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 long-form human readable name for a thing" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:order 11 ; + sh:path rdf:type ], + [ 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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct: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 "The value in this node property represents the knowledge provider that created or assembled the node 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. @@ -16483,47 +16497,33 @@ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 unique identifier 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: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 "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path rdfs:label ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ 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 unique identifier 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 description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ 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: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: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 human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path rdfs:label ], [ 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 ; @@ -16535,30 +16535,31 @@ 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: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 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: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 7 ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:full_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 8 ; sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ 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:order 13 ; + 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16568,38 +16569,37 @@ 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:NamedThing ; - sh:description "connects an attribute to a 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:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "A unique identifier 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:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ 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 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -16612,18 +16612,24 @@ 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:order 0 ; - sh:path biolink:provided_by ], + 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct: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. @@ -16633,76 +16639,46 @@ 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:order 6 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 2 ; - sh:path biolink:full_name ], + 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 0 ; + 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 6 ; + sh:path rdf:type ] ; 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: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 "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A property of a phenotype" ; + 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], - [ 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 "A unique identifier 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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ 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 3 ; - 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. @@ -16712,6 +16688,22 @@ 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: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 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:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -16719,34 +16711,59 @@ 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 "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 biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ] ; 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "a human-readable description of an entity" ; 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:order 11 ; + sh:path dct: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 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:description "a human-readable description of an 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 11 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ 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 "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ 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. @@ -16756,39 +16773,22 @@ 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 unique identifier 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: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: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 0 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ 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 7 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; @@ -16806,46 +16806,10 @@ biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_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:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct: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: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 unique identifier 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 "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - 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. @@ -16855,16 +16819,27 @@ 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: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:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path rdfs:label ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 ], @@ -16872,38 +16847,47 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t 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:path biolink:has_output ], + [ 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:order 11 ; + 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: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 6 ; + 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 0 ; + sh:path biolink:id ], + [ 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: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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 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 unique identifier 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 description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ 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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -16915,34 +16899,53 @@ 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: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 9 ; - sh:path biolink:has_attribute ] ; + 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 9 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_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 1 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct: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:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct: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:order 4 ; + sh:path biolink:full_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 5 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_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. @@ -16952,41 +16955,15 @@ 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:class biolink:Attribute ; - sh:description "may often be an organism 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 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 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 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 5 ; - sh:path biolink:id ], - [ sh:order 8 ; - sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; - sh:path rdfs:label ] ; - 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: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:class biolink:OrganismTaxon ; @@ -16994,20 +16971,49 @@ biolink:Polypeptide a sh:NodeShape ; 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 6 ; - sh:path biolink:iri ], [ sh:order 8 ; sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct: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: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: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 3 ; + sh:path biolink:xref ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_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 2 ; + sh:path biolink:provided_by ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17017,58 +17023,58 @@ 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: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 scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 10 ; + sh:path dct:description ], + [ sh:order 8 ; + 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:full_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 3 ; - sh:path biolink:xref ] ; + sh:order 6 ; + 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: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: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: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: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 6 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + sh:order 5 ; + 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 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 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + 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 "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 30 ; - sh:path dct:description ], + 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 "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:PopulationOfIndividualOrganisms ; sh:description "the population that form the object of the association" ; sh:maxCount 1 ; @@ -17076,144 +17082,155 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; 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 "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: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 "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 5 ; - sh:path biolink:publications ], + 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 "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 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 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 "Used to hold the 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_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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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:description "A unique identifier 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: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 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 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:order 21 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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 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: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:description "Used to hold the 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: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 15 ; + sh:path biolink:object_category ], + [ 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: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 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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 "A human-readable name for an attribute or entity." ; + sh:order 26 ; + sh:path biolink:iri ], + [ 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 description of an entity" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ 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:order 30 ; + sh:path dct:description ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:timepoint ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; 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 "a human-readable description of an entity" ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + 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:maxCount 1 ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], - [ sh:order 8 ; - 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: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 9 ; + 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], [ 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 long-form human readable name for a thing" ; + [ 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:order 4 ; - sh:path biolink:full_name ], + 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. @@ -17223,67 +17240,86 @@ 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 "A unique identifier 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 "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 9 ; - 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 "The human readable scientific name for the taxon of the 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 "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ] ; + sh:order 4 ; + sh:path biolink:full_name ] ; 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:description "executive summary of 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:iri ], + [ 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 "executive summary of a publication" ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:summary ], + [ 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 16 ; + sh:path rdfs:label ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:license ], + [ 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 7 ; + sh:path biolink:rights ], + [ 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 18 ; sh:path biolink:has_attribute ], - [ sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:format ], [ 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 "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 "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:id ], - [ 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:order 9 ; + sh:path biolink:creation_date ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:full_name ], + [ sh:order 15 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct:description ], + [ 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 12 ; + 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. @@ -17292,58 +17328,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:minCount 1 ; sh:order 14 ; sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:rights ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:license ], - [ sh:order 15 ; - 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 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:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + 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: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 "" ; + sh:in ( "over_the_counter" "prescription" ) ; 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 9 ; - sh:path biolink:creation_date ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + 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 13 ; 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 9 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalMixture ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ 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:order 15 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 17 ; sh:path dct:description ], - [ 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 16 ; - sh:path rdfs:label ], - [ sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ] ; - 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:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:full_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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17353,79 +17389,63 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; 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:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ 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 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 15 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - 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 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 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 12 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalMixture ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ 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:order 4 ; + sh:path biolink:trade_name ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 16 ; 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 "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 "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ] ; 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: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 "The value in this node property represents the knowledge provider that created or assembled the node 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:order 9 ; + sh:path rdf:type ], + [ 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 "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_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`, ... @@ -17434,96 +17454,104 @@ 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 description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct: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 "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + 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 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 "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 3 ; 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 1 ; - 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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ 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:path biolink:has_attribute ] ; 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 10 ; - sh:path rdfs:label ], - [ 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 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct: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 3 ; + 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 2 ; + 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_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:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], + [ 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:targetClass biolink:ProteinDomain . + +biolink:ProteinFamily a sh:NodeShape ; + sh:closed true ; + 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -17533,130 +17561,81 @@ 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: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 "The value in this node property represents the knowledge provider that created or assembled the node 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 description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct: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: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 long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:ProteinDomain . - -biolink:ProteinFamily a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - 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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct: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 3 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 10 ; + sh:order 2 ; 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 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 4 ; - 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:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ 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 "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: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:path biolink:iri ] ; 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 "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: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:order 10 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + 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 3 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 11 ; sh:path dct:description ], - [ 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: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:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + 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: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 "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: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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_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. @@ -17665,85 +17644,93 @@ 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]+$" ] ; - sh:targetClass biolink:ProteinIsoform . - -biolink:RNAProduct a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:trade_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; 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 12 ; - sh:path biolink:provided_by ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_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:nodeKind sh:IRI ; - sh:order 3 ; + 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 1 ; sh:path biolink:xref ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 10 ; - 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 11 ; - sh:path biolink:has_chemical_role ], - [ sh:description "" ; + [ sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:ProteinIsoform . + +biolink:RNAProduct a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 8 ; sh:path biolink:available_from ], + [ 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:nodeKind sh:IRI ; sh:order 19 ; 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 11 ; + sh:path biolink:has_chemical_role ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:full_name ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:order 6 ; + sh:path biolink:is_metabolite ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 4 ; sh:path rdfs:label ], - [ sh:order 16 ; - sh:path rdf:type ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 10 ; + 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 9 ; + 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 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 12 ; + 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 17 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct: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 "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 14 ; + 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. @@ -17753,89 +17740,73 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 15 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:is_metabolite ] ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:order 16 ; + 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:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:trade_name ] ; 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:order 16 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_chemical_role ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 10 ; - 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:property [ 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:max_tolerated_dose ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:is_metabolite ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + sh:order 18 ; + sh:path dct: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:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:trade_name ], + sh:order 11 ; + 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 5 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:order 13 ; + sh:path biolink:full_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:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 8 ; - sh:path biolink:available_from ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 4 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 7 ; + 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 12 ; sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:full_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 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. @@ -17845,6 +17816,35 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 15 ; 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:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:order 16 ; + sh:path rdf:type ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 6 ; + 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 9 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 8 ; + sh:path biolink:available_from ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:is_toxic ], + [ 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 17 ; @@ -17854,14 +17854,45 @@ 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:class biolink:Publication ; + sh:property [ 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 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 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 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: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 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path dct: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 14 ; + 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 28 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -17871,74 +17902,19 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; 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 17 ; - 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 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: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:nodeKind sh:IRI ; - sh:order 7 ; - 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 22 ; - 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 11 ; - sh:path biolink:primary_knowledge_source ], - [ 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: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 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: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 "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: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 1 ; - sh:path biolink:reaction_direction ], + sh:order 23 ; + 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 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: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 14 ; - sh:path biolink:original_subject ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -17946,108 +17922,168 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNode ; sh:order 5 ; sh:path rdf:object ], - [ 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 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 "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + [ 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:order 2 ; - sh:path biolink:reaction_side ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path dct: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 30 ; - sh:path biolink:category ], - [ sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 32 ; + 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:order 6 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 4 ; + 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 25 ; + sh:path biolink:subject_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 7 ; + 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 15 ; 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 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: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: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: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 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 "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:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - 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 19 ; - sh:path biolink:subject_closure ], - [ 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: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: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 0 ; - sh:path biolink:stoichiometry ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + 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 29 ; sh:path biolink:iri ], - [ 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:id ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ] ; 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 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 "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + 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 rdf:predicate ], - [ 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:order 28 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path dct: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 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:maxCount 1 ; - sh:order 16 ; - 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 12 ; + 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:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - 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:order 7 ; + sh:path biolink:qualifiers ], + [ 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: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 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 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 "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 human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 32 ; + 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 10 ; + sh:path biolink: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: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 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 25 ; + 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 24 ; @@ -18059,49 +18095,48 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; 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: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: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: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 "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 "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 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 "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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 32 ; - 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: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 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:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; + sh:order 13 ; + 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 18 ; - sh:path biolink:object_category ], - [ 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:order 8 ; + 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. @@ -18109,91 +18144,77 @@ 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 "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: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: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: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 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: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 point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - 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 21 ; + 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 29 ; 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 10 ; - 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 7 ; - sh:path biolink:qualifiers ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 31 ; - sh:path rdf:type ], - [ 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 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 "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: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 15 ; + sh:path biolink:original_predicate ], + [ 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: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:class biolink:Attribute ; + 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 4 ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ 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 "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ 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 scientific name for the taxon of the entity." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 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 rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path dct: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. @@ -18203,67 +18224,32 @@ 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:description "A human-readable name for an attribute or entity." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 10 ; + sh:order 3 ; 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: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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct: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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; + sh:path biolink:in_taxon ] ; 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 "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; + 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 unique identifier 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 ; @@ -18273,32 +18259,46 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 11 ; sh:path dct: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 "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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 1 ; + sh:path biolink:id ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:order 9 ; - 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: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 "The value in this node property represents the knowledge provider that created or assembled the node 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:path biolink:has_biological_sequence ] ; sh:targetClass biolink:RegulatoryRegion . biolink:RelationshipQuantifier a sh:NodeShape ; @@ -18321,25 +18321,10 @@ 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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ 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:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ 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 11 ; - 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:order 8 ; + 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. @@ -18349,18 +18334,28 @@ 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 0 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:full_name ], [ 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 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 4 ; + sh:path biolink:provided_by ], [ sh:maxCount 1 ; sh:order 2 ; sh:path biolink:format ], + [ sh:description "A unique identifier 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 "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:order 3 ; @@ -18368,15 +18363,20 @@ 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 "A unique identifier 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:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ] ; sh:targetClass biolink:RelativeFrequencyAnalysisResult . biolink:SensitivityQuantifier a sh:NodeShape ; @@ -18388,92 +18388,97 @@ 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: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:description "a point in time" ; + 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 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 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 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:order 11 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ 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 26 ; - sh:path biolink:iri ], + sh:minCount 1 ; + 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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: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 "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 "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ 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: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: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 12 ; - sh:path biolink:original_predicate ], + 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 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: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 "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 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 13 ; - sh:path biolink:original_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:order 10 ; + sh:path biolink:timepoint ], + [ 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 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 "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 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + 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 30 ; - sh:path dct:description ], + 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:maxCount 1 ; @@ -18481,57 +18486,52 @@ 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 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:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:retrieval_source_ids ], + 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 "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 description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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: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 "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 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 "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - 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 25 ; - sh:path biolink:id ], + 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:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting 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: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: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 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:targetClass biolink:SequenceAssociation . biolink:SequenceFeatureRelationship a sh:NodeShape ; @@ -18543,19 +18543,11 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; 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: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:description "A unique 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 rdf:object ], + sh:order 25 ; + sh:path biolink:id ], [ 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 ; @@ -18563,37 +18555,106 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; 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 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 20 ; - sh:path biolink:subject_namespace ], - [ 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 "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: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 "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 "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 "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: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: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 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: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: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: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 human-readable description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct: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: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 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 "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. @@ -18601,54 +18662,43 @@ 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 "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 "A unique identifier 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: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: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: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: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 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 "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 "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: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: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 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: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 ; @@ -18656,68 +18706,35 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t 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: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 "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:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 31 ; 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: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: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: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 point in time" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; - 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: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: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 "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:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; + 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 "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: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. @@ -18725,164 +18742,143 @@ 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: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 description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct: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 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 "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 "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: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: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: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: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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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 "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 25 ; - sh:path biolink:id ], + 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 "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: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: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: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 "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: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 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: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 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: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: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:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_attribute ], + 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 "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 5 ; + sh:path biolink:publications ] ; 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: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 "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], - [ 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:property [ sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:id ], + [ sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:order 18 ; + sh:path rdf:type ], + [ 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path dct: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 9 ; + sh:path biolink:license ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + 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 16 ; + 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 13 ; sh:path biolink:provided_by ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path dct: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: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 "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:format ], - [ sh:maxCount 1 ; - sh:order 10 ; - 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. @@ -18892,102 +18888,104 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 17 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:id ], + [ sh:maxCount 1 ; + sh:order 10 ; + 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: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 "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:summary ], [ 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:iri ], - [ sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:license ], + sh:order 12 ; + sh:path biolink:creation_date ], [ 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 "keywords tagging a publication" ; + sh:order 6 ; + 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 8 ; + sh:path biolink:xref ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 14 ; - sh:path biolink:full_name ], - [ sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:order 18 ; - sh:path rdf:type ] ; + sh:path biolink:full_name ] ; 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:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 8 ; + sh:path biolink:available_from ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct: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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 13 ; sh:path biolink:full_name ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:is_metabolite ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 12 ; + sh:path biolink:provided_by ], [ sh:description "" ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:is_toxic ], - [ 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 "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path rdfs:label ], [ 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 17 ; 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - 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:order 14 ; + sh:path biolink:iri ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 7 ; + 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 11 ; 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 14 ; - sh:path biolink:iri ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - 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 12 ; - sh:path biolink:provided_by ], - [ sh:order 16 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 8 ; - 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 15 ; + 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 ; @@ -18998,59 +18996,59 @@ biolink:SiRNA a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:trade_name ], - [ sh:description "a human-readable description of an entity" ; + sh:order 6 ; + 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 18 ; - sh:path dct: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 15 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + sh:order 9 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:order 16 ; + sh:path rdf:type ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; sh:closed true ; sh:description "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)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:order 12 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - 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 "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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:id ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], + sh:order 11 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 0 ; 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 3 ; - sh:path biolink:max_tolerated_dose ], - [ 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 5 ; - sh:path biolink:has_chemical_role ], + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; @@ -19061,67 +19059,72 @@ biolink:SmallMolecule a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; 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:description "A unique identifier 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:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:order 12 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct: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: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 value in this node property represents the knowledge provider that created or assembled the node 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. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 2 ; sh:path biolink:available_from ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ] ; + sh:order 8 ; + sh:path biolink:full_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: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: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 8 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + 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 "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:full_name ], [ 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:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path dct: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. @@ -19131,107 +19134,104 @@ 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: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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct: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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 11 ; + sh:order 4 ; 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 5 ; - sh:path biolink:provided_by ], + [ sh:order 10 ; + sh:path rdf:type ], [ 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:path biolink:has_biological_sequence ], + [ 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: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: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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct: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:property [ sh:class biolink:SocioeconomicAttribute ; + sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + 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 10 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], [ 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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:order 11 ; - sh:path rdf:type ], [ sh:description "a point in time" ; sh:maxCount 1 ; sh:order 0 ; 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 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 "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 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 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 10 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 6 ; + 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:SocioeconomicAttribute ; - sh:description "connects any entity to an attribute" ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:SocioeconomicExposure . biolink:SocioeconomicOutcome a sh:NodeShape ; @@ -19249,25 +19249,23 @@ biolink:Study a sh:NodeShape ; sh:closed true ; sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:full_name ], [ 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 description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct: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:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -19282,41 +19280,37 @@ 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: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 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:description "a long-form human readable name for a thing" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_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 1 ; - sh:path biolink:xref ] ; + sh:order 7 ; + sh:path rdfs:label ] ; 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: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 human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], - [ sh:order 8 ; - 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: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 "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 11 ; + sh:path biolink:has_attribute ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; @@ -19330,15 +19324,6 @@ 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 "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 "may often be an organism 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 2 ; sh:path biolink:provided_by ], @@ -19346,50 +19331,73 @@ 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:full_name ], - [ 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 9 ; - sh:path rdfs:label ] ; + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:order 8 ; + 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: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: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: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: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: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: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 "A human-readable name for an attribute or entity." ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path dct: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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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: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:order 10 ; - sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ 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 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 13 ; + 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. @@ -19399,64 +19407,33 @@ 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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_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:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:order 10 ; + sh:path rdf:type ] ; 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ 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: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: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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -19466,14 +19443,37 @@ 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 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:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:order 10 ; + 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: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 description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ 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:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; @@ -19485,36 +19485,57 @@ biolink:SubjectOfInvestigation a sh:NodeShape ; biolink:TaxonToTaxonAssociation 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:property [ 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 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:order 10 ; + sh:path biolink:timepoint ], + [ 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 "a human-readable description of an entity" ; + sh:order 11 ; + sh:path biolink:original_subject ], + [ 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 ; - sh:order 30 ; - sh:path dct:description ], + 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: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: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: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: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 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 "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:order 3 ; @@ -19523,48 +19544,22 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; 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: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 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: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: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:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + 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: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: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 "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 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:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + 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 ], @@ -19573,6 +19568,22 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; 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: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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -19580,48 +19591,37 @@ 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 "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 5 ; - 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 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 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 "A unique identifier 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: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 14 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path dct: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 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:OrganismTaxon ; sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; @@ -19646,34 +19646,28 @@ 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: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: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: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 11 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_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 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 13 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + 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:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:order 10 ; - sh:path rdf:type ], + 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. @@ -19683,25 +19677,31 @@ 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 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:minCount 1 ; sh:order 7 ; 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:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + [ 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 5 ; sh:path biolink:xref ], - [ 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 8 ; - sh:path biolink:iri ] ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:TextMiningResult . biolink:ThingWithTaxon a sh:NodeShape ; @@ -19723,15 +19723,50 @@ 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 "a point in time" ; + 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 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 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 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 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: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: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. @@ -19739,166 +19774,113 @@ 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: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 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 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:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + 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: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 "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path rdfs:label ], - [ 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: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 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path rdf:type ], + [ 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: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: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 "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 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 "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 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 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: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 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: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 12 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct: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: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 "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: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: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 "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 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 "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:order 7 ; + sh:path biolink:knowledge_source ] ; 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: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: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 7 ; - sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path rdfs:label ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:full_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 1 ; - 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. @@ -19913,101 +19895,111 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t 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 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 "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + 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 5 ; sh:path biolink:xref ], - [ 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 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 "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct: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:targetClass biolink:TranscriptionFactorBindingSite . biolink:VariantAsAModelOfDiseaseAssociation 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:property [ 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: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: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: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 33 ; - sh:path biolink:onset_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 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: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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path dct: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:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; + sh:order 32 ; + sh:path biolink:severity_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - 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: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 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: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 "a point in time" ; + [ 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 "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 "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: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 "The relationship to the disease" ; 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:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:subject_category ], + 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 ; + sh:path biolink:iri ], [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 28 ; sh:path rdf:type ], @@ -20016,20 +20008,25 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; 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 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 "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: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 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: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 33 ; + sh:path biolink:onset_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. @@ -20037,57 +20034,60 @@ 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 27 ; sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ 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 unique identifier 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 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:class biolink:Disease ; - sh:description "disease" ; + [ 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: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 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 relationship to the disease" ; + sh:order 0 ; + 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: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:order 34 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "a human-readable description of an entity" ; 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:order 30 ; + sh:path dct: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 13 ; - sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; + 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 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 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 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 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 7 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:IRI ; + 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 ; @@ -20099,53 +20099,58 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:closed true ; 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: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: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 7 ; - sh:path biolink:knowledge_source ], + sh:order 34 ; + sh:path biolink:frequency_qualifier ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct:description ], - [ 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 ; - sh:minCount 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 0 ; - 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:order 5 ; + sh:path biolink:publications ], + [ 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 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 "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:order 32 ; + sh:path biolink:severity_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 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: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 15 ; - sh:path biolink:object_category ], + 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:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:subject_category ], + [ 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: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 ; @@ -20156,169 +20161,122 @@ biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_evidence ], - [ 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: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 5 ; - sh:path biolink:publications ], - [ sh:description "E.g. is pathogenic for" ; + 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:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + 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 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:minCount 1 ; + sh:order 25 ; + sh:path biolink:id ], + [ 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 ; + sh:minCount 1 ; + 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 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 "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 "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:SeverityValue ; - sh:description "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; - 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 32 ; - sh:path biolink:severity_qualifier ], + 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: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 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 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 "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:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 28 ; - sh:path rdf:type ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; + sh:description "Used to hold the 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:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 15 ; + sh:path biolink:object_category ], + [ sh:description "E.g. is pathogenic for" ; 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 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 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: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: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:targetClass biolink:VariantToDiseaseAssociation . - -biolink:VariantToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:VariantToEntityAssociationMixin . - -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: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: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:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 33 ; + 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: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: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 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 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: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: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: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: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:targetClass biolink:VariantToDiseaseAssociation . + +biolink:VariantToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:VariantToEntityAssociationMixin . + +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: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: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 ; @@ -20330,79 +20288,68 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; 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: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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 7 ; + sh:path biolink: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: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 unique identifier 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: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: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:order 19 ; + sh:path biolink:object_category_closure ], + [ 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: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 "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 30 ; sh:path dct: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 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: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 20 ; - sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 26 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; 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: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: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: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 "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 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:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; @@ -20410,152 +20357,127 @@ 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 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: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: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: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: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 rdf:object ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + 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: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 1 ; - sh:path biolink:expression_site ], - [ 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 "A unique identifier 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 "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 6 ; sh:path biolink:has_evidence ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; - 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 2 ; - sh:path biolink:stage_qualifier ], + 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 21 ; + sh:order 17 ; sh:path biolink:object_closure ], - [ 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: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: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: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 relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ 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 16 ; - sh:path biolink:original_predicate ], + 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 24 ; + 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 28 ; - 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: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 "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 18 ; + sh:path biolink:subject_category_closure ] ; + 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: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 25 ; - 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 17 ; + 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 26 ; + 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 11 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + 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 18 ; 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 30 ; - sh:path biolink:iri ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 34 ; sh:path dct: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 26 ; - 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path rdfs:label ], + sh:order 35 ; + 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 15 ; 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 13 ; + sh:path biolink:aggregator_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 6 ; + 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 7 ; + 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 12 ; + 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 22 ; + 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 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 ; @@ -20566,6 +20488,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ 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 "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: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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 32 ; + 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 8 ; + sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 33 ; + 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 9 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; @@ -20578,298 +20525,355 @@ 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:phenotypic_state ], - [ 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: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: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 "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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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:primary_knowledge_source ] ; - sh:targetClass biolink:VariantToGeneExpressionAssociation . - -biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - 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:path biolink:object_category ], + [ 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 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:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 10 ; 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 21 ; - 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 18 ; - sh:path biolink:object_closure ], - [ 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: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: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:order 11 ; + sh:path biolink:knowledge_source ], + [ 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 38 ; - 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:order 2 ; + sh:path biolink:stage_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 27 ; + 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 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: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 39 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:object_category ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 31 ; sh:path dct: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:description "total number of things in a particular reference set" ; 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:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:severity_qualifier ], + sh:order 7 ; + 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 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 "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 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 "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:has_total ], - [ 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:maxCount 1 ; - sh:order 13 ; - 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 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:nodeKind sh:IRI ; sh:order 15 ; 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 10 ; - 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: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 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:minCount 1 ; + 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:order 14 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 2 ; + 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:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ 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 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 "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: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 0 ; - sh:path biolink:sex_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:order 37 ; + 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:maxCount 1 ; + sh:order 9 ; + 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 20 ; - sh:path biolink:object_category_closure ], + sh:order 25 ; + sh:path biolink:retrieval_source_ids ], + [ 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 unique identifier 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 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: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 "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 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: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: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:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_quotient ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:has_percentage ], [ 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 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: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 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 subject 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 16 ; - sh:path biolink:object_category ], - [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 12 ; + 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:order 36 ; - sh:path biolink:has_percentage ], - [ 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:order 38 ; + sh:path biolink:onset_qualifier ], + [ sh:description "if set to true, then the association is negated i.e. is not true" ; 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:order 4 ; + 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 10 ; + 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 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:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - 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 5 ; - 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 13 ; + sh:path biolink:original_predicate ], + [ 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:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + sh:order 39 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ] ; + sh:order 30 ; + sh:path rdfs:label ] ; 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 "equivalent to has quotient multiplied by 100" ; + 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 32 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_percentage ], - [ sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:order 35 ; + sh:path dct: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 24 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_count ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + 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:maxCount 1 ; + sh:order 16 ; + 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 25 ; 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 14 ; - 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: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:description "number in object population that carry a particular allele, aka allele count" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ], + sh:order 0 ; + sh:path biolink:has_count ], + [ sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_percentage ], + [ 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: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: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 "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 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: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 9 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], [ 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 "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: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: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: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 5 ; - 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 32 ; - sh:path biolink:category ], - [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:description "Used to hold the 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 2 ; - sh:path biolink:has_quotient ], - [ 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 "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 19 ; + 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:order 17 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 6 ; + 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 29 ; 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 27 ; - sh:path biolink:subject_label_closure ], + [ sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + 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 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; @@ -20877,30 +20881,15 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:nodeKind sh:IRI ; sh:order 7 ; 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 28 ; - 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 10 ; - 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 18 ; - 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 16 ; - sh:path biolink:original_subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ 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 35 ; - sh:path dct:description ], + sh:order 2 ; + 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 23 ; + 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 ; @@ -20910,51 +20899,79 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 13 ; 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 27 ; + 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 31 ; + 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 22 ; + 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 21 ; + 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 28 ; + 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 8 ; + 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 11 ; sh:path biolink:has_evidence ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + 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 26 ; 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 31 ; - 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 8 ; - 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: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 19 ; - sh:path biolink:subject_category ], - [ sh:description "number all populations that carry a particular allele, aka allele number" ; + sh:order 4 ; + 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:maxCount 1 ; - 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:description "a point in time" ; + sh:order 12 ; + 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 15 ; - sh:path biolink:timepoint ] ; + sh:order 17 ; + sh:path biolink:original_predicate ] ; 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:order 8 ; - 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:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_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 5 ; + 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -20964,68 +20981,45 @@ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 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 5 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; + [ sh:order 8 ; + 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:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - 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:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ] ; + sh:order 10 ; + sh:path dct: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: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:order 8 ; - sh:path rdf:type ], + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism 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 3 ; 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -21035,18 +21029,26 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + 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:class biolink:Attribute ; - sh:description "may often be an organism 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 6 ; 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 7 ; + 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 ; @@ -21056,48 +21058,38 @@ 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:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ] ; + [ sh:order 8 ; + sh:path rdf:type ] ; 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 "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:maxCount 1 ; + sh:property [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:format ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], + [ 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:order 15 ; sh:path rdf:type ], - [ 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 ], + [ 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 18 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ 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 12 ; - 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -21107,68 +21099,85 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ 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 "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 16 ; - 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:minCount 1 ; + sh:order 12 ; + sh:path biolink:id ], [ sh:maxCount 1 ; sh:order 6 ; sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path dct: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 10 ; - sh:path biolink:provided_by ], + sh:order 13 ; + 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 9 ; + 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 0 ; + sh:path biolink:authors ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:rights ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct:description ], [ sh:description "keywords tagging a publication" ; sh:order 3 ; sh:path biolink:keywords ], - [ 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:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ 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 13 ; - sh:path biolink:iri ] ; + sh:order 16 ; + sh:path rdfs:label ] ; sh:targetClass biolink:WebPage . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + 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 rdfs:label ], + sh:order 9 ; + 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 "A unique identifier 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: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 "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_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: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 6 ; sh:path biolink:provided_by ], + [ 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:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; @@ -21183,26 +21192,17 @@ biolink:Behavior a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], + [ sh:order 11 ; + 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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 12 ; sh:path rdfs:label ], - [ 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:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - 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 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. @@ -21218,32 +21218,26 @@ 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 2 ; - sh:path biolink:provided_by ], - [ 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 "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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:order 8 ; sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct: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. @@ -21256,20 +21250,26 @@ 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 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + 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: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 2 ; + sh:path biolink:provided_by ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ] ; sh:targetClass biolink:BehavioralFeature . biolink:BiologicalProcess a sh:NodeShape ; @@ -21279,146 +21279,140 @@ biolink:BiologicalProcess a sh:NodeShape ; 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:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + [ 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:enabled_by ], + 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 10 ; + 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 12 ; + sh:path rdfs:label ], + [ sh:order 11 ; + 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: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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 human-readable description of an entity" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:order 11 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path rdfs:label ], [ 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:full_name ], + [ 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 6 ; + 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 14 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + [ 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:full_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. + sh:order 9 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 10 ; + sh:order 7 ; 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:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path rdfs:label ], - [ 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: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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 10 ; + sh:path dct: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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 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 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 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], [ sh:order 8 ; sh:path rdf:type ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; 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 7 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; - sh:targetClass biolink:Case . - -biolink:CellLine a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ 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:full_name ], + sh:order 6 ; + 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 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 0 ; sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:Case . + +biolink:CellLine a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The human readable scientific name for the taxon of the 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 human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; @@ -21432,109 +21426,103 @@ 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:order 8 ; - 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct: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 2 ; sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_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 5 ; 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 6 ; - sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ 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 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism 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 2 ; - 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 3 ; + sh:path biolink:xref ], + [ 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 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 2 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - 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:maxCount 1 ; sh:order 6 ; 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 3 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 9 ; + sh:order 1 ; sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + 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 7 ; + 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 5 ; sh:path biolink:id ], - [ sh:order 8 ; - sh:path rdf:type ] ; + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ] ; 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: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 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], @@ -21544,8 +21532,32 @@ biolink:ClinicalAttribute a sh:NodeShape ; 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: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: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 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct: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. @@ -21561,40 +21573,53 @@ 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 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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; + 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; + 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:full_name ], + [ 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:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ 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: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: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:order 13 ; + sh:path biolink:has_attribute ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; @@ -21602,38 +21627,15 @@ biolink:Dataset 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 5 ; sh:path biolink:xref ], - [ 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 "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], - [ 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 8 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], [ sh:description "A unique identifier 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 "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. @@ -21642,57 +21644,46 @@ 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:order 10 ; - sh:path rdf:type ] ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; sh:targetClass biolink:Dataset . 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 1 ; - 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: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 8 ; sh:path biolink:id ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:format ], - [ 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:order 11 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 2 ; - 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 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 10 ; + 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 5 ; 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:maxCount 1 ; + sh:order 1 ; + sh:path biolink:license ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:distribution_download_url ], + [ 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; @@ -21701,35 +21692,49 @@ biolink:DatasetDistribution a sh:NodeShape ; sh:maxCount 1 ; sh:order 13 ; sh:path dct: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 10 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; + [ sh:maxCount 1 ; + 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 14 ; + sh:path biolink:has_attribute ], + [ sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:format ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + 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 6 ; + sh:path biolink:xref ] ; 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives 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: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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 6 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh: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:full_name ], - [ 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: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. @@ -21739,64 +21744,40 @@ 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:description "A unique identifier 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 0 ; + sh:path biolink:provided_by ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct: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 "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], [ 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:path rdfs:label ] ; 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:order 15 ; - sh:path rdf:type ], - [ 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct: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: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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], + sh:order 13 ; + sh:path biolink:iri ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:trade_name ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_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. @@ -21806,82 +21787,105 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; 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: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: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 "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 3 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path rdfs:label ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 16 ; sh:path rdfs:label ], - [ sh:description "indicates whether a molecular entity is a 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 4 ; - sh:path biolink:is_metabolite ], + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], + [ sh:order 15 ; + sh:path rdf:type ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 6 ; sh:path biolink:available_from ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 13 ; - 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 1 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:order 4 ; + sh:path biolink:is_metabolite ], + [ sh:description "" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct: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 11 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ] ; + sh:order 12 ; + sh:path biolink:full_name ] ; 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 "The value in this node property represents the knowledge provider that created or assembled the node 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:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + 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:maxCount 1 ; sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct: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: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 4 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], + sh:order 12 ; + 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 2 ; @@ -21895,52 +21899,49 @@ 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 description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 5 ; + sh:path biolink:full_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 3 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; 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:order 9 ; - sh:path rdf:type ] ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ] ; 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: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 "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:path rdfs:label ] ; sh:targetClass biolink:GeneProductMixin . 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:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 description of an entity" ; sh:maxCount 1 ; sh:order 10 ; @@ -21950,14 +21951,6 @@ biolink:GeneticInheritance a sh:NodeShape ; 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: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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -21969,65 +21962,69 @@ 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 "a long-form human readable name for a thing" ; + [ 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:full_name ], + 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 2 ; + sh:path biolink:provided_by ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 1 ; sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_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 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 0 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:xref ] ; 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 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:property [ sh:description "A human-readable name for an attribute or entity." ; 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:order 11 ; + 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 8 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:maxCount 1 ; sh:order 1 ; sh:path biolink:rights ], + [ sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "A unique identifier 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 "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ 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: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: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 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -22037,12 +22034,15 @@ 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 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: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:maxCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 6 ; @@ -22053,26 +22053,26 @@ 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:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - 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: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 0 ; + sh:path biolink:in_taxon ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh: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:full_name ], + 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 3 ; + 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. @@ -22082,29 +22082,29 @@ 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:order 8 ; - 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct: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 "may often be an organism attribute" ; 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:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + 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 6 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:order 8 ; + sh:path rdf:type ] ; sh:targetClass biolink:OrganismalEntity . biolink:Outcome a sh:NodeShape ; @@ -22121,100 +22121,97 @@ biolink:PredicateMapping a sh:NodeShape ; 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 9 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_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:order 17 ; + sh:path biolink:species_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 0 ; - sh:path biolink:mapped_predicate ], + sh:minCount 1 ; + sh:order 7 ; + sh:path rdf:predicate ], [ 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 14 ; - sh:path biolink:object_context_qualifier ], + sh:order 3 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:object_derivative_qualifier ], + sh:order 4 ; + sh:path biolink:subject_part_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:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ], + [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_direction_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:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_derivative_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:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_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:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_derivative_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: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:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:broad_match ], - [ 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:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualified_predicate ] ; + sh:order 10 ; + sh:path biolink:object_direction_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:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:narrow_match ], + [ sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:object_context_qualifier ], + [ sh:maxCount 1 ; + 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 0 ; + sh:path biolink:mapped_predicate ], + [ 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: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:order 6 ; - sh:path rdf:type ], - [ 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 7 ; - sh:path rdfs:label ], - [ 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: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 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 ], @@ -22222,13 +22219,10 @@ biolink:Procedure a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a human-readable description of an entity" ; 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 1 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path dct: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. @@ -22238,55 +22232,28 @@ 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 description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ] ; + 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 9 ; + 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: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: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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct: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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 10 ; - 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:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; @@ -22304,16 +22271,49 @@ 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:full_name ], + [ 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 "A unique identifier 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: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 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:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; 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: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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:Treatment a sh:NodeShape ; @@ -22327,11 +22327,16 @@ biolink:Treatment a sh:NodeShape ; sh:maxCount 1 ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:Device ; - sh:description "connects an entity to one or more (medical) devices" ; + [ sh:description "A unique identifier 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 1 ; - sh:path biolink:has_device ], + 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 5 ; sh:path biolink:xref ], @@ -22340,78 +22345,57 @@ biolink:Treatment a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_procedure ], - [ sh:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ 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:order 6 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:iri ], [ 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:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Device ; + sh:description "connects an entity to one or more (medical) devices" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:order 10 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:has_device ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ 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 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 8 ; - sh:path biolink:iri ] ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:Treatment . biolink:Zygosity a sh:NodeShape ; sh:closed true ; 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 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:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 11 ; + sh:path dct: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 8 ; - sh:path biolink:full_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 6 ; - sh:path biolink:provided_by ], + 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. @@ -22421,95 +22405,102 @@ 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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ 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 12 ; - sh:path biolink:has_attribute ], - [ 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 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 "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:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNode ; + sh:order 2 ; + sh:path biolink:has_quantitative_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:order 5 ; - sh:path biolink:id ], - [ 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 human-readable description of an entity" ; + 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 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; 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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_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 14 ; - 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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:has_attribute ], + [ sh:order 15 ; + sh:path rdf:type ], [ sh:class biolink:ChemicalEntity ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; 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 7 ; - sh:path biolink:max_tolerated_dose ], [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - 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 13 ; - sh:path biolink:iri ], + sh:order 8 ; + 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 9 ; + 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 0 ; sh:path biolink:id ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + [ 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:drug_regulatory_status_world_wide ], - [ 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 7 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], - [ 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:order 16 ; + sh:path rdfs:label ], + [ 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:full_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 11 ; sh:path biolink:xref ], @@ -22519,25 +22510,34 @@ 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: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 4 ; - sh:path biolink:routes_of_delivery ], + [ 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 "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 14 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ 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 8 ; - sh:path biolink:is_toxic ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path rdfs:label ], - [ sh:order 15 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ] ; + sh:order 13 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Drug . biolink:ExposureEvent a sh:NodeShape ; @@ -22559,39 +22559,38 @@ 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 "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 human-readable description of an entity" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:order 8 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:full_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 2 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - 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:description "The human readable scientific name for the taxon of the 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 1 ; - sh:path rdfs:label ], + 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 3 ; sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ 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 6 ; + sh:path biolink:iri ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 9 ; + 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. @@ -22601,34 +22600,42 @@ 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 "A unique identifier 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:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:order 8 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 11 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ] ; 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 "a human-readable description of an entity" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct: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 2 ; + sh:path biolink:full_name ], [ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 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. @@ -22638,179 +22645,100 @@ 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:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], [ 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:description "A unique identifier 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 1 ; - sh:path biolink:xref ] ; + 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 "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ] ; 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 human-readable description of an 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 17 ; - sh:path dct: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: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 biolink:max_tolerated_dose ], + sh:order 16 ; + sh:path rdfs:label ], + [ 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 13 ; sh:path biolink:iri ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; + [ sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - 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 14 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 8 ; + 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 7 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 2 ; 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 15 ; - sh:path rdf:type ], [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:order 4 ; 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "" ; + [ sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], + sh:order 12 ; + sh:path biolink:full_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:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_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 10 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + 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 9 ; sh:path biolink:has_chemical_role ], + [ sh:order 15 ; + sh:path rdf:type ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 6 ; - sh:path biolink:available_from ] ; - sh:targetClass biolink:Transcript . - -biolink:Pathway a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - 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 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: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 unique identifier 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:order 11 ; - sh:path rdf:type ], + 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 7 ; + sh:order 11 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ 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: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 "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; sh:order 5 ; - sh:path rdfs:label ], - [ 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:path biolink:trade_name ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; + sh:order 17 ; sh:path dct: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. @@ -22818,126 +22746,219 @@ biolink:Pathway a sh:NodeShape ; This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 10 ; + sh:order 14 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ] ; - sh:targetClass biolink:Pathway . + sh:targetClass biolink:Transcript . -biolink:LifeStage a sh:NodeShape ; +biolink:Pathway a sh:NodeShape ; sh:closed true ; - sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives 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 unique identifier 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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 10 ; + 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: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:xref ], - [ sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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 description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; + 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 14 ; + sh:path biolink:has_attribute ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; + sh:order 12 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - 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 6 ; + 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 4 ; - sh:path biolink:full_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:path biolink:in_taxon ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 5 ; + 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:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:class biolink:Attribute ; + sh:path biolink:xref ], + [ sh:order 11 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Pathway . + +biolink:LifeStage a sh:NodeShape ; + sh:closed true ; + sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 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 0 ; sh:path biolink:in_taxon ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_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 3 ; + 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 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 6 ; + sh:path biolink:iri ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:order 8 ; sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; - sh:path dct:description ] ; + sh:path dct: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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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: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 11 ; - sh:path biolink:xref ], + 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 14 ; + sh:path biolink:category ; + sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:is_metabolite ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + 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 7 ; 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:order 15 ; + 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 11 ; + sh:path biolink:xref ], + [ 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: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 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 9 ; sh:path biolink:has_chemical_role ], - [ sh:order 15 ; - sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path rdfs:label ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 16 ; 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 14 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + 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 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 10 ; + sh:path biolink:provided_by ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 12 ; sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:description "indicates whether a molecular entity is a metabolite" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_metabolite ], + sh:order 17 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -22946,43 +22967,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - 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 10 ; - 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 13 ; - sh:path biolink:iri ] ; + sh:path biolink:has_biological_sequence ] ; 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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], + 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:description "A unique identifier 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:order 8 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + 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. @@ -22992,39 +23001,30 @@ 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 "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 "may often be an organism 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 6 ; - sh:path biolink:iri ], - [ sh:order 8 ; - 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: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 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 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; + sh:order 9 ; sh:path rdfs:label ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . @@ -23038,14 +23038,23 @@ 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: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 "The value in this node property represents the knowledge provider that created or assembled the node 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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: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 unique identifier 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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_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. @@ -23055,99 +23064,92 @@ 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: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:MolecularEntity ; + sh:description "A chemical entity that is the input for the reaction" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 1 ; + sh:path biolink:has_input ], + [ 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 "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:description "A unique identifier 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 "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:order 5 ; sh:path rdfs:label ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + [ sh:order 11 ; + sh:path rdf:type ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 13 ; sh:path dct:description ], + [ 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:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + 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:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:order 11 ; - sh:path rdf:type ], - [ 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:path biolink:has_attribute ] ; 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 "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalEntity ; + sh:property [ sh:class biolink:ChemicalMixture ; 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: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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - 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 "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:order 13 ; + 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 7 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalMixture ; - sh:description "" ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 11 ; + sh:path biolink:full_name ], + [ 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:order 15 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an 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 17 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + 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. @@ -23157,36 +23159,10 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; 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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - 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 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ 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 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 12 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; @@ -23194,7 +23170,31 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t [ 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:path biolink:drug_regulatory_status_world_wide ], + [ 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 "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 16 ; + 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 9 ; + sh:path biolink:provided_by ], + [ 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 description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct: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:targetClass biolink:ChemicalMixture . biolink:MacromolecularMachineMixin a sh:NodeShape ; @@ -23212,44 +23212,50 @@ biolink:MolecularEntity a sh:NodeShape ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], [ 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:order 12 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + 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 10 ; - sh:path biolink:iri ], + sh:order 3 ; + 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 6 ; sh:path biolink:provided_by ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 13 ; 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:order 12 ; + 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 9 ; + sh:path biolink:id ], + [ sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + 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. @@ -23259,68 +23265,57 @@ 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:ChemicalEntity ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - 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 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "indicates whether a molecular entity is a metabolite" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 14 ; + sh:path dct:description ], + [ sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:order 0 ; + sh:path biolink:is_metabolite ] ; sh:targetClass biolink:MolecularEntity . 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 "a human-readable description of an entity" ; + 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ 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 "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 0 ; sh:path biolink:in_taxon ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -23335,28 +23330,50 @@ 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:order 8 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 6 ; - 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 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PhenotypicFeature . 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct: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:description "The value in this node property represents the knowledge provider that created or assembled the node 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 3 ; - sh:path biolink:id ], + 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 1 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -23366,48 +23383,66 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:full_name ], - [ 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 4 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ] ; + sh:targetClass biolink:PhysicalEntity . + +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 long-form human readable name for a thing" ; 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 0 ; - sh:path biolink:provided_by ], + sh:path biolink:full_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 5 ; + sh:order 9 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:order 6 ; - sh:path rdf:type ] ; - sh:targetClass biolink:PhysicalEntity . - -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:class biolink:Attribute ; + [ sh:class biolink:Zygosity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ 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: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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:order 8 ; @@ -23417,33 +23452,39 @@ biolink:Genotype a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:class biolink:Zygosity ; - sh:maxCount 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 6 ; + sh:path biolink:xref ] ; + 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: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_zygosity ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:has_gene ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path rdfs:label ], - [ sh:order 10 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path dct: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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 8 ; + sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:full_name ], + [ 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 ], @@ -23451,18 +23492,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:maxCount 1 ; sh:order 11 ; sh:path rdfs:label ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ] ; - 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:order 10 ; + [ 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 13 ; + 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. @@ -23472,63 +23508,43 @@ 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 unique identifier 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 description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path rdfs:label ], - [ 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 "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - 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 6 ; - 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: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 human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "The state of the sequence w.r.t a reference sequence" ; + 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:maxCount 1 ; - sh:order 1 ; - 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 5 ; - sh:path biolink:provided_by ] ; + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ] ; 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ], + [ sh:order 8 ; + 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 6 ; sh:path biolink:iri ], @@ -23536,10 +23552,15 @@ biolink:Agent a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:address ], - [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; + [ 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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path dct: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. @@ -23549,32 +23570,11 @@ 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:order 8 ; - 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:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_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 2 ; - sh:path biolink:provided_by ], - [ 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: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 5 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct: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 ] ; @@ -23584,27 +23584,45 @@ 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: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: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 6 ; + 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 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 5 ; + sh:path biolink:id ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path rdfs:label ], [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct: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:description "The value in this node property represents the knowledge provider that created or assembled the node 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: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. @@ -23614,35 +23632,22 @@ 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: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 0 ; - sh:path biolink:in_taxon ], - [ 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:description "The human readable scientific name for the taxon of the 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:path rdfs:label ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeature . 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:description "a human-readable description of an entity" ; + sh:property [ 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 human-readable description of an entity" ; sh:maxCount 1 ; sh:order 10 ; sh:path dct:description ], @@ -23650,6 +23655,13 @@ biolink:Disease a sh:NodeShape ; sh:maxCount 1 ; sh:order 9 ; sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_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 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. @@ -23659,10 +23671,21 @@ 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:order 8 ; + 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 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 5 ; + sh:path biolink:id ], + [ sh:description "The human readable scientific name for the taxon of the 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 ], @@ -23670,62 +23693,24 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t 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 human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - 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:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:order 8 ; - 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:path biolink:in_taxon ] ; sh:targetClass biolink:Disease . biolink:BiologicalSex a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + 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 "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ 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 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct: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. @@ -23735,6 +23720,26 @@ 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ 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 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 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 ; @@ -23742,45 +23747,52 @@ 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 "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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_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 7 ; - sh:path biolink:xref ], - [ 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 5 ; - sh:path biolink:id ] ; + 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: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:targetClass biolink:BiologicalSex . 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 "connects a genomic feature to its sequence" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - 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 5 ; - sh:path biolink:in_taxon ], - [ sh:order 11 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 13 ; + sh:path dct:description ], + [ sh:description "Symbol for a particular thing" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:symbol ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 1 ; + 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 3 ; + 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 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. @@ -23790,76 +23802,49 @@ 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 "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 rdfs:label ], + [ sh:description "The human readable scientific name for the taxon of the 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 14 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 1 ; - 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: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 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 5 ; + sh:path biolink:in_taxon ], + [ 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 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 4 ; - sh:path biolink:id ], - [ sh:description "Symbol for a particular thing" ; - 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 9 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:Gene . 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 6 ; - sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an 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 10 ; - sh:path dct: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:order 8 ; - sh:path rdf:type ], + 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. @@ -23869,80 +23854,78 @@ 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 "A unique identifier 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 long-form human readable name for a thing" ; + [ 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:full_name ], + sh:order 6 ; + 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 9 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:order 8 ; + 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:order 10 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:full_name ], [ 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 "A unique identifier 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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + [ sh:order 10 ; + 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 "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct: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: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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 ], @@ -23950,10 +23933,27 @@ 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 human-readable description of an entity" ; + [ 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. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:ChemicalRole . biolink:GeneOrGeneProduct a sh:NodeShape ; @@ -23980,19 +23980,13 @@ biolink:Onset a sh:NodeShape ; sh:maxCount 1 ; sh:order 11 ; sh:path dct: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:Attribute ; - sh:description "connects any entity to an 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 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 6 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; @@ -24005,13 +23999,11 @@ biolink:Onset a sh:NodeShape ; sh:maxCount 1 ; sh:order 0 ; 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 1 ; - sh:path biolink:has_attribute_type ], + [ sh:order 10 ; + 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. @@ -24021,55 +24013,40 @@ 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 7 ; - sh:path biolink:xref ], - [ 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 5 ; - sh:path biolink:id ] ; - 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:class biolink:QuantityValue ; + [ 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 10 ; - 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 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 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:has_attribute ] ; + 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 long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ 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. @@ -24079,10 +24056,34 @@ 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: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 "The value in this node property represents the knowledge provider that created or assembled the node 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 unique identifier 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 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:Attribute ; + sh:description "connects any entity to an attribute" ; + 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 4 ; @@ -24094,10 +24095,9 @@ 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 human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct: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:targetClass biolink:SeverityValue . biolink:QuantityValue a sh:NodeShape ; @@ -24118,50 +24118,51 @@ 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 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: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 human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "a human-readable description of an entity" ; + sh:order 12 ; + 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 13 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:iri ], + [ 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: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 8 ; - 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: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:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:order 13 ; + sh:path dct:description ], [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:full_name ], - [ sh:order 11 ; - sh:path rdf:type ], + [ 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 "" ; 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 8 ; + 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. @@ -24171,49 +24172,25 @@ 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 human-readable name for an attribute or entity." ; + [ sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalEntity ; + sh:description "" ; sh:maxCount 1 ; - 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 "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ] ; + 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: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: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 long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path dct: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 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 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. + 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`, ... @@ -24222,57 +24199,66 @@ 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path dct:description ], + [ sh:order 6 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_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 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: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: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: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 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 "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + 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: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 "A unique identifier 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 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 description of an entity" ; sh:maxCount 1 ; sh:order 8 ; sh:path dct: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 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. @@ -24281,47 +24267,71 @@ 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: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 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 3 ; + sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ] ; 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: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 8 ; + sh:path biolink:iri ], + [ sh:order 10 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 11 ; 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 description of an 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 12 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 7 ; + 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 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 4 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:maxCount 1 ; sh:order 0 ; sh:path biolink:license ], + [ 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: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 "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 12 ; + sh:path dct: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. @@ -24331,43 +24341,26 @@ 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: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 7 ; - sh:path biolink:id ], [ sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:rights ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:path biolink:rights ] ; 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 "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:iri ], - [ sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:creation_date ], - [ 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:order 2 ; + sh:path biolink:summary ], + [ 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:minCount 1 ; - sh:order 12 ; - sh:path biolink:id ], - [ sh:order 15 ; - 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 10 ; - sh:path biolink:provided_by ], + sh:order 16 ; + 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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -24377,97 +24370,88 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t sh:order 14 ; sh:path biolink:category ; sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:order 15 ; + 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:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:maxCount 1 ; + sh:order 6 ; + 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 11 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:iri ], [ sh:maxCount 1 ; sh:order 8 ; sh:path biolink:format ], - [ 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:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path dct: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: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 "executive summary of a publication" ; + [ 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: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:minCount 1 ; + sh:order 12 ; + sh:path biolink:id ], [ sh:maxCount 1 ; sh:order 7 ; sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], - [ 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 16 ; - 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 "The value in this node property represents the knowledge provider that created or assembled the node 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: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:description """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. - * In a neo4j database this MAY correspond to the neo4j label tag. - * In an RDF database it should be a biolink model class URI. -This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... -In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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:property [ 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 12 ; - sh:path biolink:category ; - sh:pattern "^biolink:[A-Z][A-Za-z]+$" ], + sh:order 1 ; + sh:path biolink:resource_role ], [ 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 "The value in this node property represents the knowledge provider that created or assembled the node 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:order 13 ; - sh:path rdf:type ], - [ 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 "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 "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:order 14 ; sh:path rdfs:label ], - [ sh:maxCount 1 ; - sh:order 4 ; - 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 7 ; + 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 8 ; + sh:path biolink:provided_by ], [ 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 ; @@ -24476,40 +24460,58 @@ 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: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 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:maxCount 1 ; - sh:order 6 ; - 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 7 ; - sh:path biolink:creation_date ], - [ 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: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 """Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class 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 1 ; - sh:path biolink:resource_role ], + 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:maxCount 1 ; sh:minCount 1 ; sh:order 10 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path dct:description ], + [ sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:format ], + [ sh:order 13 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], + [ 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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: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:description "The value in this node property represents the knowledge provider that created or assembled the node 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: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 ; @@ -24517,10 +24519,10 @@ biolink:Attribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:full_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. @@ -24533,41 +24535,39 @@ 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 7 ; sh:path biolink:xref ], - [ sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_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 5 ; sh:path biolink:id ], + [ 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: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 2 ; sh:path biolink:has_quantitative_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:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path dct: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: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 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; diff --git a/biolink-model.ttl b/biolink-model.ttl index 1acd4ca04b..47db4dacca 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -349,268 +349,268 @@ , , ; - linkml:generation_date "2023-06-30T20:57:05"^^xsd:dateTime ; + linkml:generation_date "2023-06-30T21:13:40"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mmmp.biomaps" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HANCESTRO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NBO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "orphanet" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema1: ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference dcat: ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MESH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-TOPIC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], + linkml:prefixes [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD9" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "HCPCS" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OMIM.PS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXNORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], + [ linkml:prefix_prefix "UNIPROT.ISOFORM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-TOPIC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NBO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ComplexPortal" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HsapDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTEx" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "os" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CLINVAR" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foaf" ; - linkml:prefix_reference foaf: ], - [ linkml:prefix_prefix "FYPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.food" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.CHEMICAL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBbt" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNOMEDCT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXCUI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.compound" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "AGRKB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UniProtKB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SPDI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "STY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MmusDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSSG" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ncats.drug" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "WBls" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "wgs" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ORCID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.PATHWAYS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHAROS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "schema" ; + linkml:prefix_reference schema1: ], [ linkml:prefix_prefix "PANTHER.FAMILY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "issn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "REPODB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "DrugCentral" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MESH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "AGRKB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "doi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ECTO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mmmp.biomaps" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_CORE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.VARIANT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UO-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Xenbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DGIdb" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ChemBank" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "MmusDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ScopusID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEMMEDDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCIT-OBO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "PomBase" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.RCLASS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "METANETX.REACTION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.DISEASE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "LOINC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "bioschemas" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.CHEMICAL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EFO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CTD.CHEMICAL" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "PMC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEED.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "qud" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.VARIANT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "UBERON_NONAMESPACE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "metacyc.reaction" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "apollo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.PATHWAY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "XPO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "AspGD" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.PATHWAYS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DrugCentral" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcid" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.PATHWAY" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "EDAM-OPERATION" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBls" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ECTO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Xenbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UNIPROT.ISOFORM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "FYECO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GSID" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VMC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UMLSSG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ResearchID" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ncats.bioplanet" ; linkml:prefix_reference ], [ linkml:prefix_prefix "prov" ; linkml:prefix_reference prov: ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHAROS" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "CHADO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBbt" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "dcid" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.food" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VANDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference foaf: ], + [ linkml:prefix_prefix "STY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gff3" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "orphanet" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNOMEDCT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference dcat: ], + [ linkml:prefix_prefix "CTD.DISEASE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "XPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gtpo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXCUI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "metacyc.reaction" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COAR_RESOURCE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "MI" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERGRAPH" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "linkml" ; linkml:prefix_reference linkml: ], - [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VMC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COAR_RESOURCE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gtpo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MAXO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORCID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EFO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ComplexPortal" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCIT-OBO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VANDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mirbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "PHARMGKB.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "interpro" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "KEGG.GENES" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "DGIdb" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HsapDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "bioschemas" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERON_CORE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD.DISEASE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DOID-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "METANETX.REACTION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "medgen" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OMIM.PS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHARMGKB.DISEASE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "SPDI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MAXO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PMC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CLINVAR" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UniProtKB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "biolink" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ] ; + [ linkml:prefix_prefix "medgen" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.compound" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DOID-PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "FYECO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEED.REACTION" ; + linkml:prefix_reference ] ; linkml:slots , , , @@ -1313,7 +1313,7 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "2023-06-30T20:55:19"^^xsd:dateTime ; + linkml:source_file_date "2023-06-30T21:12:12"^^xsd:dateTime ; linkml:source_file_size 356212 ; linkml:subsets , , @@ -2123,9 +2123,9 @@ 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 ; @@ -2579,9 +2579,9 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:example "blood" ], + skos:example "cerebral cortext" ], [ a linkml:Example ; - skos:example "cerebral cortext" ] ; + skos:example "blood" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -12118,11 +12118,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "increases response to" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "increases response to" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12473,11 +12473,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "True" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "has not completed" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "True" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12568,11 +12568,11 @@ skos:inScheme ; skos:narrowMatch ; linkml:annotations [ a linkml:Annotation ; - skos:example "has decreased amount" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "has decreased amount" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -12720,11 +12720,11 @@ 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 ; @@ -12945,11 +12945,11 @@ skos:exactMatch ; skos:inScheme ; linkml:annotations [ a linkml:Annotation ; - skos:example "decreases response to" ; - linkml:tag ], - [ a linkml:Annotation ; skos:example "True" ; - linkml:tag ] ; + linkml:tag ], + [ a linkml:Annotation ; + skos:example "decreases response to" ; + linkml:tag ] ; linkml:definition_uri ; linkml:domain ; linkml:inherited true ; @@ -13230,11 +13230,11 @@ 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 ; @@ -13560,11 +13560,11 @@ 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 ; @@ -14054,11 +14054,11 @@ ; 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 ; @@ -15330,11 +15330,11 @@ 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 ; @@ -15353,13 +15353,13 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; + skos:example "abundance" ], + [ a linkml:Example ; skos:example "stability" ], [ a linkml:Example ; skos:example "exposure" ], [ a linkml:Example ; - skos:example "expression" ], - [ a linkml:Example ; - skos:example "abundance" ] ; + skos:example "expression" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -15487,9 +15487,9 @@ 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 ; @@ -15616,15 +15616,15 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "severe" ], + skos:example "transplant" ], [ a linkml:Example ; - skos:example "mutation" ], + skos:example "severe" ], [ a linkml:Example ; skos:example "chemical analog" ], [ a linkml:Example ; skos:example "late stage" ], [ a linkml:Example ; - skos:example "transplant" ] ; + skos:example "mutation" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -16171,9 +16171,9 @@ linkml:definition_uri ; linkml:domain ; linkml:examples [ a linkml:Example ; - skos:example "polyA tail" ], + skos:example "upstream control region" ], [ a linkml:Example ; - skos:example "upstream control region" ] ; + skos:example "polyA tail" ] ; linkml:is_a ; linkml:owner ; linkml:range ; @@ -16802,11 +16802,11 @@ 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 ; @@ -18706,9 +18706,9 @@ , ; 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:owner ; linkml:range ; @@ -23642,11 +23642,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "annotation predicate" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "predicate" ; - linkml:local_name_source "translator" ] ; + linkml:local_name_source "translator" ], + [ a linkml:LocalName ; + skos:altLabel "annotation predicate" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; diff --git a/biolink/model.py b/biolink/model.py index 0c2814e944..201c89480f 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: 2023-06-30T20:57:19 +# Generation date: 2023-06-30T21:13:51 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model diff --git a/context.jsonld b/context.jsonld index 4f127c7075..abdcf5ddab 100644 --- a/context.jsonld +++ b/context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-06-30T20:56:23", + "generation_date": "2023-06-30T21:13:05", "source": "biolink-model.yaml" }, "@context": { diff --git a/contextn.jsonld b/contextn.jsonld index b603c3b008..718b425c5f 100644 --- a/contextn.jsonld +++ b/contextn.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-06-30T20:56:28", + "generation_date": "2023-06-30T21:13:10", "source": "biolink-model.yaml" }, "@context": {